Khan was responding to the Prime Minister Narendra Modi's plan to connect Madarasas to mainstream education.
The MP told reporters that "Madrasas do not breed people with Nathuram Godse's nature or with a personality like Pragya Thakur".
"First announce that those propagating thoughts of Nathuram Godse will be declared enemies of democracy, those convicted for terror activities will not be rewarded," Azam Khan added.
Pragya Thakur, an accused in the 2008 Malegaon blasts and out on bail, won the recent Lok Sabha election from Bhopal as a BJP candidate. She remained in the news for claiming that Nathuram Godse, who killed Mahatma Gandhi in 1948, was a "patriot".
Azam Khan said if the central government wanted to help Madarasas, then they should bring about improvements.
"Religious teaching is given at Madarasas. At the very same Madarasas, English, Hindi and Maths are also taught. This has always been done. If you want to help, improve their standard. Build buildings for Madarasas, provide them with furniture and midday meals," he said.
Union Minister Mukhtar Abbas Naqvi, while announcing the scheme, had said. "Madarasas are in large numbers across the country. They will be connected with the formal education and mainstream education so that those children studying there can also contribute in the development of the society."
He explained that Madarasa teachers across the country would be given training from various institutions in subjects like Hindi, English, Maths, Science and Computers.
As part of its outreach to minorities, the government will give out five crore scholarships for the education of minorities over the next five years and half the beneficiaries will be girl students.
( With inputs from IANS )