The crackdown came in response to a UN Security Council resolution passed last month, describing Jamaat-ud-Dawa as a "terror group".
Malik also said that Islamabad needed more information from India in order to proceed with its own investigations into last November's attack on the Indian financial capital.
"This is the time that Pakistan and India need to stick together," he said. "We'll be needing more information."
More than 170 people died when several locations in Mumbai, including two famous hotels, came under simultaneous attacks.