A division bench comprising Chief Justice J N Patel and Justice S Chakraborti refused to pass any interim stay.
It was hearing a PIL filed by Asim Sarkar, general secretary of West Bengal unit of BJP challenging the government's decision to pay a monthly allowance to all imams in the state.
The bench also directed the disbursing authority to inform beneficiaries to be aware that if the petition was allowed, those who took the benefit of the scheme in the interim period, would have to return the money.
The state government was directed to file its affidavit in opposition by May 18 and the petitioner to file its affidavit in reply by June one.
The next hearing would be held on June eight.
Chief Minister Mamata Banerjee had last month announced that all imams would be paid Rs 2,500 per month as honorarium.