"Pakistan has conveyed its grave concern to India over (the) unnecessary delay in the free and fair investigation of Samjhauta Express terrorist attack," the Foreign Office said in a statement.
"We also call upon the Indian government to share information about the investigation proceedings of the terrorist attack," it said.
More than 42 Pakistani nationals lost their lives in the bombings, the statement said.
It said that the "Indian attempts to exonerate some of the individuals" involved in the attacks have raised serious questions over the due process of law and dispensation of justice.
NIA has filed charge sheet against eight people including Naba Kumar Sarkar alias Swami Asimanand, Sunil Joshi (deceased), Ram Chandra Kalsangra, Sandeep Dange and Amit (absconding), Lokesh Sharma, Kamal Chauhan and Rajender Choudhary in the case which is under trial.