"Monks don't have rights to freely give sermons nor form their own organizations. Monks are losing their rights," he said. He did not say whether he intended to challenge the directive.
The rise of groups such as those led by Wirathu have been a consequence of the religious and ethnic conflicts, and many believe in turn that their ideology further inflames the problem.
The situation presents a dilemma for the government, which faces calls from human rights groups and Western nations to take decisive measures to curb religious intolerance and violence in which hundreds of people have been killed and more than 100,000 displaced in the past year.
But Wirathu's movement is popular and its anti-Muslim sentiments are shared by many. There is also an admired tradition of activism by Buddhist monks dating back to British colonial times, and they spearheaded some anti-military activities under the junta that yielded power two years ago.
The junta banned monks' organizations in 1990 after Mandalay-based monks boycotted the military and their families by staging a campaign to reject traditional alms from them. The campaign was launched after the authorities suppressed public demonstrations by monks.
Mandalay is the traditional center of Buddhist social and political activism.
The State Sangha Nayaka Organization was formed in 1980 during the rule of the late dictator Ne Win.