Foreign Office (FO) said that Deputy High Commissioner JP Singh met the Director General (SA& SAARC), who lodged a protest against the decision of the National Investigation Agency (NIA) to not oppose the bail granted to Aseemanand on "Special Leave Permission."
"The Government of Pakistan has serious reservations on the efficiency of the Court in processing and disposal of cases regarding terrorism, especially those involving deaths of Pakistani citizens," the foreign office said.
The Samjhauta Express, the only rail link between India and Pakistan, was bombed in February, 2007.
Four Improvised Explosive Devices were planted on the Samjhauta Express, a twice-weekly train service connecting Delhi, India, and Lahore, Pakistan on February 18, 2007, in which 68 lives were lost.
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The NIA decided not to oppose the conditional bail to Assemanand as it did not find any grounds for it, Minister of State for Home Haribhai Parathibhai Chaudhary had informed the Lok Sabha earlier this week.
Pakistan action comes ahead of the talks between the National Security Advisors on August 23 on terror-related issues and is an indication of Islamabad's plan to rake up issues like 2007 Samjhauta Express bombings.
Later, Singh was summoned again to lodge a protest over the killing of a woman in alleged ceasefire violations by India, sources said.
Pakistan today claimed that Indian Border Security Force (BSF) opened "unprovoked firing" at Line of Control (LoC) in Nezapir sector of Rawalakot, killing one woman and injuring her husband and two daughters.