The court's observation came while hearing a PIL filed by gay activists seeking to decriminalise gay sex among consenting adults.
Additional Solicitor General P P Malhotra, appearing for the Centre, cited an article which contained quotes from religious texts to justify the ban.
Not satisfied with the Government contention, the Bench, also comprising Justice S Muralidhar, asked the government to show scientific proof that gay sex is harmful to society.
"This is just one-sided version of a religious body which cannot be relied upon. This is part of religious doctrine. Show us some scientific report which says that gay sex should be criminalised," a Division Bench headed by Chief Justice A P Shah said.
Earlier, the Centre had justified the criminal provision against homosexual acts and had said that it is required to curb the spread of HIV infection.
The petitioner, Naz Foundation, an NGO, had said that Section 377 which criminalises homosexual acts is unconstitutional and it should be amended to allow gay sex among consenting adults.
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