Shinde's directive in a letter to the Chief Ministers was condemned by the Opposition as "votebank politics" with BJP alleging it was done keeping the upcoming Lok Sabha elections in mind. BJP demanded that Shinde be sacked for attempting to divide the country on communal lines and the directive be withdrawn immediately.
In the letter, 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.
"Government has to ensure that no innocent person is subjected to undue harassment," he told the Chief Ministers.
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Shinde asked the state governments to constitute special courts in consultation with the high court concerned for trial of terror-related cases, appoint special public prosecutors for trial of these cases and give priority to them 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.
"Had he used the word Indian instead of any religion then it would have been better. Shinde should be sacked with immediate effect for dividing the country on communal lines," BJP General Secretary Rajiv Pratap Rudy told reporters.
Senior BJP leader M Venkaiah Naidu alleged that Shinde has written this letter for votebank politics and keeping the forthcoming elections in mind.
He said Shinde's move is "unconstitutional and questionable" and demanded that the directive should be taken back immediately.