Larger organisations will have to register with the commission by March 2008, and the smallest before March 2010.
The new commission, set to be established in June, will issue guidance on the public benefit test that applicants in the province must pass.
Organisations seeking charitable status have been told they will have to undergo a "rigorous test" of whether their activities benefit the public.
The order stresses that it "will not be presumed that a particular purpose is for the public benefit".
Paul McGill, communications officer at the Northern Ireland Council for Voluntary Action, welcomed the test, which he said would "reassure people that charities are helping the public as a whole, and not just a minority group".