That bombing last month triggered a dangerous escalation that last week pushed Pakistan and India close to an all-out war over Kashmir. In Tuesday's statement, the ministry says 44 suspects were arrested, including prominent members of the outlawed militant group. Among those arrested was Mufti Abdul Rauf, the brother of the group's leader, Masood Azhar.
The ministry says the brother was among suspects listed in a file on the February bombing that India gave to Pakistan over the weekend. Kashmir is split between Pakistan and India and is claimed by both in its entirety.
Pakistan's navy says it spotted and warned an Indian submarine approaching its territorial waters in the Arabian Sea not to attempt an incursion.
The navy said in a statement Tuesday that the Indian submarine wasn't targeted, "keeping in view Pakistan's policy of peace" under which Islamabad wants to de-escalate tensions with New Delhi.
A navy official says the warning was "communicated" to the submarine during Monday's encounter. The submarine then moved away. He didn't elaborate and spoke on condition of anonymity to talk to reporters.
Tension escalated after India last week launched an airstrike inside Pakistan, claiming it targeted militants behind a Feb. 14 bombing in Indian-controlled Kashmir that killed 40 Indian troops.
Pakistan retaliated by downing two Indian fighter jets and capturing a pilot who was later handed back.