Foreign Office spokesperson Tasnim Aslam told the Geo TV in Islamabad that it would be unfortunate if the investigations were "unifocal."
"It should be investigated through all angles," she said.
While she preferred not to "speculate" over who was behind the blasts, Aslam said it was unlikely that any Pakistani nationals would have gone to India and carried out the attack as most of those killed or injured were from Pakistan.
She also denied allegations that the critically injured passengers who were being treated in New Delhi's Safdarjung hospital were flown back in haste.
"I do not know who said this. It is very surprising," Aslam said.
She said when Foreign Minister Khurshid M Kasuri visited the injured on February 20, he told the doctors that they would be consulted before shifting the patients.
Pakistan made arrangements for the shifting of those injured only after taking doctors' advice and being informed of facilities required for the patients on board the aircraft.
Railway Minister Sheikh Rashid said according to the details he had with him, all those killed in the two compartments were Pakistanis and there were no Indians passengers present.