The court also asked Pakistani authorities to extradite the suspects, but Pakistan has ruled out transferring any Mumbai suspects to India, saying it will try them in its own courts.
The warrants were issued in response to a prosecutors' motion in the ongoing trial of Mohammed Ajmal Kasab.
Prosecutors say Kasab is the only surviving gunman from last November's attacks that left 166 people dead.
|A Pakistani court freed Hafiz Mohammed Saeed earlier this month [AFP]
Pakistan had arrested the three leaders in December after Indian diplomats provided a dossier of evidence in a rare sharing of intelligence between the nuclear-armed rivals.
However, earlier this month, a court in the eastern city of Lahore freed Saeed, saying there was no evidence against him.
New Delhi says the 10 gunmen involved in the Mumbai attacks were Pakistanis and that their handlers in Pakistan kept in touch with them by phone during the three-day assault on 10 sites across the city including two five-star hotels and a Jewish centre.
Indian officials have also accused Pakistani intelligence agents of involvement in the attacks — a charge denied by Islamabad, although it has acknowledged that the Mumbai attacks were partly plotted on Pakistani soil.