The professorships, which come with no extra funding but enable universities to use the title, are to be awarded for excellence in teaching and research in a particular discipline.
Some 44 Regius professorships already exist across the UK and Ireland, traditionally created when a university chair is founded or endowed by a Royal patron.
Such professorships exist at the universities of Aberdeen, Cambridge, Edinburgh, Glasgow, Oxford, and St Andrews in the UK and at Trinity College Dublin in Ireland. Any universities in the UK will be able to apply for the new positions.
According to the Cabinet Office, applications, which must be made by the vice-chancellor or chancellor, will be judged on the university's excellence in the proposed discipline and on the recognition that work in that discipline has gained, regardless of how long it has been studied.
Other factors, such as the chance to mark a significant event in the history of the discipline or institution, will also be considered but with a lower weighting.
On top of the six positions announced today, the Queen has also agreed to create an additional Regius professorship of engineering at Cambridge in recognition of the service to the university of her husband, the Duke of Edinburgh, who retired as chancellor last year.
The last Regius position created before the current announcement was in 2009 when Cambridge was also allowed to re-designate an existing professorship as a Regius professorship to mark the university's 800th anniversary and the 200th anniversary of the birth of Charles Darwin.
Before that the last professorship was created by Queen Victoria.
Applications, open until 23 November, will be judged by a panel of academics led by Sir Graeme Davies, chair of the Higher Education Policy Institute and former vice-chancellor of the University of London.
The panel will advise the minister for political and constitutional reform, Chloe Smith, and minister for universities and science, David Willetts, on applicants' merits, who in turn will advise the Queen.
"Bestowing a Regius professorship is a tremendous and exceptional honour," said Mr Willetts. "I'm extremely pleased that the Queen will be using her Jubilee year to recognise the outstanding quality of teaching and research that UK higher education institutions can offer. "
Results of the competition will be announced in early 2013.