He also asked Prime Minister Manmohan Singh to advise his cabinet colleague not to focus his attention on minorities alone as "principles at stake" could not be sacrificed "at the altar of political expediency".
In a letter to Singh, the BJP's prime ministerial contender said Shinde's statement could send a wrong message about the country's criminal justice system and have a demoralising effect on the law enforcement machinery.
"The suggestion (from Shinde) is unprecedented and marks a new low for the country.... The principles at stake are far too valuable to be sacrificed at the altar of political expediency," he said.
The Gujarat Chief Minister said, "a crime is a crime irrespective of the birth marks of the criminal and his religious beliefs could not determine the guilt or innocence."
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Shinde had last week made a statement that he would write to all state governments to set up review or screening committees to assess the role of minority youths languishing in jails on terror charges without trial.
Modi also wrote that the suggestion was against the constitutional principle of right to equality before law.