Foreign Office spokesman Nafees Zakaria made the remarks at a media briefing here, a day after Aseemanand was acquitted along with six others in the 2007 Ajmer blast case.
"Aseemanand made a public confession in 2010 that he was the mastermind of Samjhauta attack, along with Abhinav Bharat's head, Col Purohit, who was serving army officer," Zakaria said and termed Aseemanand's acquittal in the Ajmer blast case as "regrettable".
Aseemanand is an accused in the Samjhauta blast case.
Zakaria said India had assured Pakistan at the highest level that it will punish the culprits of the train bombing.
"We were given assurance at the highest political level on numerous occasions that India will share investigations on this attack with us, but we didn't hear anything from them," the spokesman said.
"What we have noted is that over the last few years they had been exonerating people involved in the Samjhauta Express terrorist attack," he said.
A member of right-wing Hindu group Abhinav Bharat, Assemanand has been in jail since December 2010. He was also named as an accused in Hyderabad Mecca Masjid blast case.
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