Captain James Cook was to exploration what Linford Christie was to Lycra.

He stretched and defined it, made it a macho subject of competitive national pride and recast it as deeply sexy.

In three brilliant voyages between 1768 and 1779, Cook, the son of a farm labourer, redrew the map of the known world, from Arctic to Antarctic, discovered new lands, refined knowledge of those barely contacted, and dispelled for ever the myths of a mysterious southern continent that was held to counterbalance the vast landmasses of the northern hemisphere and the existence of the northwest passage through the Arctic to Asia. In the Navy, Cook was appreciated for his charts. Through his writings he became famous and well off. And through his death at the hands of Hawaiians, he became a martyr to just about any noble value the West cared to espouse, most notably the Enlightenment project of throwing a net of knowledge over the globe.

But to be famous and a national hero in one age is to be notorious and a criminal in international law in the next, so that, as values have shifted, Cook has become a villain to the champions of the victims of the colonisation and dispossession that followed in his wake. Even Cook himself, as the locals variously embraced him, adored him, attacked him or - in the case of Australian aborigines, simply ignored him - became more aware of the dire effects of western contact.

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In recent years, Cook has been reglossed by a number of stern post-colonial writers and assessed as simply evil. A more balanced treatment is long overdue, yet it is curious that the same publisher has simultaneously commissioned not one but two studies that rework this already familiar ground. Since both authors are Antipodean, there is a sense in which their coming to terms with Cook parallels their own voyages of self-discovery through pre-anthropological guilt.

The main problem with Cook from a biographer's point of view is that he did too much and he was untidy, retracing his own steps and visiting the same places over and over. Nicholas Thomas takes us by the hand and gently leads us through all three expeditions. There is an understated mastery in the way he handles the numerous versions, editions and accounts to reveal the reporters' discomfort and dissimulation, half-truths and downright lies.

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His vision is deeply moral. Did Sir Joseph Banks, who would become the most powerful scientist of his day, callously abandon his servants to freeze to death in Tierra del Fuego? Probably. Was Cook arrogantly trigger-happy? Yes and no. In the anthropological vision, moral relativism is still the dominant stance, so on what basis are we to judge two colliding world-views, both situated in the past? Thomas wriggles uncomfortably with the problem, as did Cook, and musters clear condemnation only when treating the forced prostitution of their women by Maori men.

He argues convincingly that Cook was slowly transformed from surveyor to ethnographer by his exotic encounters, in ways that created a gulf between him and his crew, leading him to sentimentalise the relations he had established with South Sea Islander elites and making the old imperialist vision of Cook - as a man undone by his own humanity - partly defensible.

Like Captain Kirk, Cook knew the loneliness of command and the burdens of the first directive. He emerges as serious, dedicated, secular, occasionally peevish and irascible, but constantly evolving, absorbing influences from both natives and fellow passengers, and usually anxious to protect locals from the crew. Having risen through the ranks, Cook had few illusions about seamen. Thomas notes that whenever he refers to the infamous massacre and eating of his men in New Zealand, Cook prefaces it with an exculpation of the Maoris and then writes them up as "good people despite their actions". Perhaps this would be a fitting epitaph for Cook himself.

That Thomas can sift through so much complex material without brutal abbreviation, or - worse - the kind of tedious frame-by-frame analysis that makes works on film studies unreadable, is a powerful argument for respect.

That he can preserve the sense of the wonder and terror that marked what were voyages to other worlds, in the midst of this Jesuitical search for sin, is an even stronger one. Thomas ranges widely over the history and art of the period, and the ethnography of the Pacific region, to produce an account that is balanced, judicious and authoritative. He steers a middle course through the ill-tempered and largely circular debates that have festered over Pacific cannibalism and the violent death and dismemberment of Cook in Hawaii.

There is a joyful irony in Thomas' probing of seamen's convoluted folklore as they set off, official torchbearers of the Enlightenment vision, to dispel the fog of ignorance and bring home the pure crystal of truth.

Arriving in Polynesia, drunken, sex-crazed seamen bicker and outbid each other, in a manner that would shame even the Guggenheim, for the curiosities that are now revered Cook treasures in our hushed museums. So great was their zest for what we now call "ethnographic art" that it fuelled a war among the Maori. In this account, Banks is revealed as rather more human than previously, lavishly "tasting the local wine" in Tahiti and dumping his fiancee on his return over doubts that she could now satisfy him sexually, and arranging for a female "assistant", disguised as a man, to join him on his second trip - alas cancelled.

Thomas wisely preserves enough 18th-century periwiggery to amuse. "Excuse the paper," writes one naval correspondent, "it's gilt, I assure you, but the cockroaches have pissed upon it." The newspapers were as reptilian then as now, swiftly converting discussions over moral universals into stories of romps with sex-crazed dusky beauties in paradise at taxpayers' expense.

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The sensationalisation of Tahitian sexuality had been set running by Louis-Antoine de Bougainville, with his tales of Eden, and there was just no stopping it. We see Cook, who battled vainly to preserve the islanders from venereal disease, just as vainly arguing against this view of promiscuous South Seas womanhood.

Thomas prefers a good story to a bad one and is eager to show locals as active partners in the encounters. Thus the famous Tahitian scene in which "A fellow above 6 feet high lay with a little girl about ten or 12 years of age publickly" was not evidence of native shamelessness but street theatre satirising the behaviour of roistering British tars. As in the public "performance" of cannibalism by a Maori on the deck of Cook's ship, they were deliberately playing up to westerners. Meanwhile, in London, public opinion would have none of such subtleties and Mrs Hayes' trendy brothel offered "the rites of Venus as practised at Taheite".

Anne Salmond's book begins with the trial of a "cannibal dog" aboard the consort ship Discovery on Cook's last trip around the world. She sees this incident as subaltern contempt for Cook's refusal to take revenge for the massacre and eating of some of their companions on the previous expedition at Grass Cove, New Zealand. Both Pacific Islanders and British officers united in their condemnation of Cook's stoic bearing of the insult and invitation of the Maori perpetrator aboard his ship. But the dog-eating was not just an expression of hostility to Maoris, it was emblematic of the way the seamen had been changed by their exotic contacts. On Cook's ships, dog meat had become acceptable food, as it was in much of the Pacific, and when he suffered a near-fatal digestive complaint, a dog was fed to Cook himself.

This shibboleth becomes the dominant theme of the book: "passive natives" are really active, adaptable and clever, using their new friends as a scarce resource. British tars cease to be British and are easily deceived.

Interpretation is mutual misunderstanding.

If anything, Salmond ranges even wider than Thomas in her explorations.

Voyages previous to Cook's are included, as is a plasterer's mate's summary of Georgian England, and she draws heavily on synoptic reconstructions of ancient Polynesian society and political history to suggest how they saw the arrival of these strange vessels. Ethnographic knowledge, that most discredited commodity, becomes the touchstone that converts incomprehensibility into inevitability and, unlike Thomas' forensic probings, Salmond accepts most of the European testimony at face value. The Maori encounter becomes the focus of interest and is seen as the fatal event that leads Cook into escalating violence towards natives and crew.

Yet there is little evidence for this. It is as likely to have been a more general adaptation to the aggression and arrogance of both Tongan and Maori culture that drove Cook to excess. On his last trip we see him behaving more and more like a fieldworker, pushily documenting secret knowledge.

Salmond's lengthy examination of Cook's muddled death in Hawaii offers little that is new. The fact remains that the part of Cook's journal leading up to this period mysteriously disappeared and so, by chance or design, we are unlikely to get to the bottom of it. Salmond sees his slaying on the beach as due as much to a collapse of command and hostility from his own marines as to the complex cosmological ideas of the Hawaiians who saw Cook as some kind of reincarnation of the peaceful god Lono, inopportunely returning to the island at a time when the god of war was on the ascendant. Perhaps we can be simpler yet. At the crucial moment, when Cook is trapped on a rock with hostile locals baying at his heels, he cannot dive into the sea to save himself because he cannot swim. Among sailors, it was considered an unlucky skill to acquire. So much for the Enlightenment project.

Nigel Barley is an anthropologist and writer, formerly at the British Museum.