Intelligence officials said the 15 men were rounded up in a series of raids early on Saturday on religious schools and hostels in the crowded port city of Karachi.
"There is a possibility that some of them have links with Jemaah Islamiyah," the official said.
"We are in touch with the concerned Indonesian and Malaysian agencies," he added.
The official said the arrested suspects had been under surveillance for several weeks, suspected of activities "not in Pakistan's national interests."
Allegedly tied to al-Qaida, Jemaah Islamiyah is blamed for a string of attacks in Indonesia and elsewhere, including the blasts in Bali last year that left 202 people dead.
Several of its members are reported to have undergone military training at al-Qaida camps in Afghanistan and studied in Pakistani religious schools.