Security personnel overpowered him and bundled him out of the auditorium after he refused to be silent.
Soon after Manmohan Singh finished his speech at the inauguration of National Waqf Development Corporation, the man rose up, protesting that minority schemes were not being implemented and the Prime Minister should stop launching new schemes.
He later identified himself as Faheem Baig, a doctor and social activist living in Jafrabad in northeast Delhi.
Baig told reporters he had written 150 letters to the Prime Minister, sharing his grievances and seeking an audience, but he had not receive even an acknowledgment.
He claimed that according to an RTI reply, a major scheme for minorities was still in the "pipeline" in his district despite being launched years ago.
"I tried everything possible to share my views with the government. I had no other option," he said, justifying his protests.
PMO sources said they have taken his representation and are looking into it.