"The person, who is the culprit has to say and not Rajnath Singh...whoever is heading the state must assume moral responsibility," Khan told reporters here without naming Modi.
Khan talking to reporters on the sidelines of the first meeting of the National Monitoring Committee for Minorities.
He also attacked the Gujarat Chief Minister for using "flowery language", which he said, would not satisfy people.
"Making flowery speeches, like what we see in drama, will not satisfy people or going to help," he said, reiterating that the Gujarat Chief Minister must accept responsibility for the 2002 communal riots.
Khan announced that educational scholarship scheme,offered by the Minority Affairs Ministry, would be completely funded by the ministry from the next fiscal after it allegedly faced hurdles in Gujarat.
According to him, the centrally sponsored scholarships for minorities students would be delivered as a central scheme from the next financial year, reducing the share of state governments in the programme.
"Earlier, 25 per cent of the pre-primary scholarships was funded by the state government. We have found that some state governments, particularly Gujarat, refuse to implement the scholarships," he said.
Khan also claimed that his ministry has approved three lakh applications under the scheme from Gujarat this year, though the quota for the state was only one lakh.
Earlier, Khan launched the 'Padho Pardesh', a scheme of interest subsidy on educational loans for overseas studies, availed by students belonging to minority communities.