It is not clear whether the ministerial decree means that followers of Ahmadiyah can continue to worship privately without "spreading" their faith.
"There has been no dissolution," Supanji said on Monday.
The activities prohibited include "the spreading of the belief that there is another prophet with his own teachings after prophet Muhammad".
Ahmadiyah followers believe the sect's founder, Mirza Ghulam Ahmad, was the final prophet of Islam and not Muhammad.
On Monday a protest by thousands of Muslims warned of a holy war against Ahmadiyah in protests outside police headquarters in central Jakarta.
The protesters carried banners calling members of Ahmadiyah "infidels" that should be "exterminated".
Critics will see the step as a failure by the government of Susilo Bambang Yudhoyono, the president, to uphold Indonesia's secular values and constitutional guarantees of religious freedom.
In Indonesia Ahmadiyah followers number only about 200,000 out of a total population of about 230 million.
They have been practising the faith in Indonesia since the 1920s.