Those on the list will be subject to training and security checks.
The controversial proposal, seen by The Sunday Telegraph, was leaked in a draft of the government's counter-extremism strategy.
The document is due out this autumn.
It says it will "require all faiths to maintain a national register of faith leaders" and that the government will "set out the minimum level of training and checks" that faith leaders will have to go through.
Registration will be compulsory for any faith leaders that want to work in the public sector, including universities.
In practice this would cover almost all faith leaders as many people often deal with the public.
A spokesperson from the Catholic Church said that it had not been consulted on the proposals and another anonymous source said the proposals would be "firmly resisted".
Maulana Shah Raza, the Imam who was a founding member of the Mosques and Imams National Advisory Board, a body designed to promote best practice, warned the government "not to meddle in religious affairs or to expand the state's involvement in deciding on religious and theological issues."
Speaking in The Sunday Telegraph, he went on to say: "The Government needs to concentrate on ensuring that safeguards are in place to protect the public and treating all faith communities equally."
The document defines extremism as "the vocal or active opposition to fundamental British values, including democracy, the rule of law, individual liberty, and the mutual respect and tolerance of different faiths and beliefs."
This crackdown has come to light a week after the Government announced it had killed two British Islamic State fighters by a drone strike.