Home Secretary Charles Clarke has used the Royal Prerogative to stop two British men freed from Guantanamo Bay being issued with passports.
Royal Prerogative also covers the declaration of war
The decision means Martin Mubanga and Feroz Abbasi are effectively confined to Britain, but their citizenship is not affected.
BBC News analyses the Royal Prerogative, which has only been used 13 times since 1947 to refuse passports, the last being 1976.
Q: What are Royal Prerogatives?
A series of historic powers officially held by the Queen that have, in reality, been passed to politicians.
They enable decisions to be taken without the backing of, or consultation with, Parliament.
Q: Why are so many people unaware of them?
Until recently, they were shrouded in mystery, with requests to reveal them refused by the government.
But, in a bid for greater accountability and transparency, a list was published in 2003 when the Commons Public Administration Committee managed to obtain the information from the Department of Constitutional Affairs.
Q: What are the powers?
In domestic matters, the Royal Prerogative covers
- the issuing and withdrawal of passports
- the appointment and dismissal of ministers
- the appointment of Queen's Counsel
- the granting of honours
- the appointment and regulation of the civil service
- the commissioning of officers in the armed forces
- the dissolution of Parliament
- the calling of elections
In foreign affairs, it covers
- the declaration of war
- the making of treaties
- the recognition of foreign states
- the accreditation of diplomats
It also allows the deployment of armed forces in the UK and abroad.
The Royal Prerogative of Mercy used to enable the withdrawal of the death penalty, but now allows changes in sentences.
It was used by then Northern Ireland Secretary Peter Mandelson to free an IRA man responsible for the Docklands bombing.
One of the more unusual parts of the prerogative is the Royal ownership of swans.
Q: Have there been challenges to the Royal Prerogative?
Former Labour MP Tony Benn believed they should be abolished and such important decisions subject to parliamentary scrutiny.
In relation to the war in Iraq, there was a vote on whether Britain should participate - but the result was only advisory, not binding.
Q: Will these powers be restricted in future?
The government has said that new prerogative powers cannot be invented.
Some have become redundant and not expected to be used again, such as the power to press gang men into the Royal Navy.
Some of the powers have been diluted by new legislation or judicial review.