Talking to reporters after the meeting, Swaraj said she raised two main issues with Malik.
"I asked him about the slow pace of the investigation into the 26/11 case and the persecution of Hindus in Pakistan who are coming to India as refugees. On 26/11 Malik informed me that there is a difference between perception and reality. The challans have been presented and the delay is by the courts," Swaraj said.
The BJP leader said Malik has asked the Pakistan ambassador to cooperate in handling cases of Hindus who are fleeing Pakistan.
She said Malik has invited her to Pakistan.
Swaraj maintained that during her conversation with Malik the latter told her he had not compared 26/11 with the Babri mosque demolition and that he has been misquoted.
The issue of Captain Saurabh Kalia, whose mutilated body was handed over by the Pakistani forces during the Kargil War, also came up for discussion between the two leaders.
Swaraj is understood to have asked Malik to ensure that those guilty of breaking the Vienna convention be brought to book.