In a letter sent to chief ministers of all states on Monday, Union Home Minister Sushil Kumar Shinde asked them to avoid detaining innocent Muslim youth wrongfully.
Shinde said the Central Government has been receiving representations about alleged harassment of innocent Muslim youth by law enforcement agencies, and added that there is a growing feeling of alienation in the community.
“Minority youth have started feeling that they are deliberately targeted and deprived of their basic rights," he added.
"Government has to ensure that no innocent person is subjected to undue harassment," he told the chief ministers.
He urged state governments to set up special courts in consultation with the concerned high court for trial of terror-related cases, appoint special public prosecutors for trial of these cases and give priority to terror cases over other pending cases.
Shinde said law enforcement agencies should be satisfied with regard to communal and social harmony while ensuring zero tolerance for terrorism.
He also called for strict and prompt action against erring police officers.
In May, the central government has set up the 39 special courts under the NIA Act to take up terror-related cases.