Security agencies must be more transparent while detaining terror suspects, the Shahi Imam of the 17th-century Jama Masjid here told Modi during their half hour meeting at the prime minister's residence.
He said a large number of Muslim youths were languishing in jails on terrorism charges.
Bukhari also took up the issue of the minority character of the Aligarh Muslim University and the Jamia Millia Islamia.
He told Modi that the government's stand in the Supreme Court on their minority character had created grave concern among Muslims.
"We urged the prime minister that the government should review its stand.
"The prime minister has promised to consider the issues, and said his government won't take any step that may put communal harmony at stake," Bukhari said.