In a letter to Chief Ministers, Shinde said Central government has been receiving various representations on alleged harassment of innocent Muslim youth by law enforcement agencies.
"Some of the minority youth have started feeling that they are deliberately targeted and deprived their basis rights," he wrote.
The Home Minister emphasised that the government is committed to its core principle of combating terrorism in every form and manifestation.
"Government has to ensure that no innocent person is subjected to undue harassment," he told the Chief Ministers.
Shinde asked the state governments to constitute special courts in consultation with 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.
The Home Minister said law enforcement agencies should be satisfied with regard to communal and social harmony while ensuring zero tolerance for terrorism.
"Strict and prompt action against erring police officers where there is malafide arrests of any member of minority community, wrongfully arrested, person should not only be released immediately but they should be suitably compensated and rehabilitated to join the mainstream," he said.
In May, the central government has set up the 39 special courts under the NIA Act to take up terror-related cases.
Minority Affairs Minister K Rahman Khan had also written to Shinde expressing concern over "wrong arrests" of Muslim youths in different parts of the country in terror cases.
Apprising the Home Ministry of the concerns expressed by various Muslim bodies that the "draconian" provisions of the Unlawful Activities Prevention Act can be misused against minorities, Khan had proposed setting up of special courts to ensure speedy trial of all terror cases.
Fully backing the Minority Affairs Minister's suggestion of setting up of special courts, Shinde wrote back to him saying, "You have my assurance that this will happen".
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