The Pakistanis belonging to the Mehdi Foundation had fled their country in April 2007 fearing prosecution on charges of blasphemy as they follow multi-faith spiritual belief that promotes doctrine of divine love.
A Union home ministry official appearing on Thursday before a bench headed by Chief Justice A P Shah said the applications for political asylum submitted in November last year was rejected.
The ministry of external affairs had been informed about it and it would initiate due procedure to deport them to Pakistan, the official said.
After coming to India, the members had staged a protest at Jantar Mantar in the capital and burnt their Pakistani passports.
They had approached the Delhi High Court in November 2008, requesting it stop the Union home ministry action to repatriate them after withdrawing cases of illegal entry and other charges.
The court disposed of the case after issuing direction to the government to initiate appropriate action to deport them at the earliest.
The Mehdi Foundation International Organisation had filed the petition before the high court on behalf of the Pakistanis.