Pakistan on Thursday said the acquittal of a Hindu radical — accused of masterminding the deadly 2007 Samjhota Express bombing — in a separate case is "regrettable".

An Indian court on Wednesday handed down a rare 'guilty' verdict to three Hindu extremists over the 2007 bombing of the Ajmer Sharif Dargah, but cleared Swami Aseemanand, the alleged mastermind of the attack initially blamed on Islamist groups.

Naba Kumar Sarkar, better known by his nickname Swami Aseemanand, the alleged ringleader behind the religiously motivated attack, was among seven Hindu extremists acquitted after prosecutors failed to prove their guilt.

Aseemanand remains in prison pending trial over his role in two separate bomb attacks — one on a mosque and another on the Samjhota Express — that together killed nearly 75 people.

"Aseemanand and Col Rohit were involved in the Samjhota Express tragedy ... Aseemanand himself confessed to the crime," FO spokesman Nafees Zakaria recalled at his weekly briefing on Thursday.

He also said Pakistan had provided complete information regarding the arrest of Indian spy Kulbhushan Jadhav to Indian authorities, but despite that, India has so far not issued a response on the matter.

Also read: Case for Indian spy’s prosecution being prepared

'Unprovoked' LoC firing

The FO spokesperson condemned repeated instances of 'unprovoked' firing by Indian troops across the Line of Control (LoC) and slammed the targeting of civilian populations.

Pakistani authorities have recorded their protest by repeatedly raising the issue of ceasefire violations with Indian officials, the FO spokesman added.

"Through such steps, Indian wants to divert the world's attention from its atrocities against [India-held] Kashmir civilians."

India has violated the ceasefire a total of 1,400 times since 2013, Zakaria said. "India violated the ceasefire 400 times in 2016 alone," he added.

Pakistan condemns 'cowardly' Kabul attack

Pakistan condemned Wednesday's terrorist attack on a hospital in Kabul which killed over 35 people as a "cowardly act".

"We pray for the victims and express our heartfelt condolences to the bereaved families," Zakaria said at the Thursday briefing.

Gunmen dressed as medics stormed the 400-bed Sardar Mohammad Daud Khan hospital in the Afghan capital on Wednesday and battled security forces for hours, killing more than 38 people and wounding dozens in an attack claimed by the militant Islamic State group.