A special National Investigation Agency (NIA) court in India's Haryana state on Wednesday acquitted four individuals accused in the Samjhota Express bombing case, Indian media reported.

In addition, an application filed on March 11 by Pakistani resident, Rahila Wakil, was dismissed by the court. The application had sought permission for out-of-court testimonies of Pakistani witnesses in the case.

“The NIA Special Court has concluded that the investigating agency has failed to prove the conspiracy charge and ruled that [the] accused deserve a benefit of [the] doubt,” The Indian Express quoted NIA Counsel RK Handa as saying.

According to NDTV, the Samjhota Express train was headed from Delhi to Lahore. Nearly 70 people were killed in the blasts, which took place near Panipat in Haryana on February 18, 2007.

The explosions ripped through the train as it was on its way to Attari in Amritsar, the last railway station on the Indian side.

At least 42 Pakistanis were among the victims of the terrorist attack.

According to NDTV, Haryana police had registered a case, but the probe was handed over to the National Investigation Agency in July 2010, which then filed a charge sheet in June 2011 after conducting a probe, indicting eight individuals.

NIA's probe came to the conclusion that the accused were upset with previous attacks on Hindu temples — Gujarat's Akshardham, Jammu's Raghunath Mandir, and Varanasi's Sankat Mochan Mandir — and had conspired to target the Pakistan-bound train as revenge, according to NDTV.

"The accused had conspired and propounded a theory of 'bomb ka badla bomb' (a bomb for a bomb)," NDTV quoted the NIA as stating in the charge sheet.

The accused include Naba Kumar Sarkar alias Swami Aseemanand, Lokesh Sharma, Kamal Chauhan, and Rajinder Chaudhary, all of whom appeared before the court.

Sunil Joshi, the alleged mastermind of the attack, was killed in December 2007, according to The Indian Express and Times of India.

The remaining three accused, namely Ramchandra Kalsangra, Sandeep Dange, and Amit, continue to be at large and have been declared as proclaimed offenders, The Indian Express reported.

The trial first began in 2010 at the Panchkula NIA court and over the course of the proceedings, around 224 witnesses of the total 299 have all testified before the court, the publication further stated.

The Samjhota Express, also known as the Attari Express, runs between Delhi and Attari in India and Delhi and Lahore in Pakistan, on Wednesdays and Sundays.

'Highly condemnable'

The Foreign Office spokesperson after news of the acquittal emerged, termed the development as "highly condemnable".

"We have received reports that 4 of the accused in the Samjhota Express bombing have been let go. This is highly condemnable," said FO spokesperson Dr Mohammad Faisal.

"What will we tell the families of the 42 Pakistanis who were killed in the attack?" he said in regret adding that this was "an extreme step" taken by India.

The spokesperson said that the Foreign Office was gathering details regarding the development and will soon release a statement in response to the verdict.

Pakistan summons Indian high commissioner

According to a press release issued by the Foreign Office (FO), the acting foreign secretary summoned India's high commissioner today in order to lodge Pakistan's protest and condemnation against the acquittal of the four accused, including Swami Aseemanand, who the FO described as "the main perpetrator" and an "activist of the Hindu terrorist organisation RSS".

The FO said the acquittal "makes a travesty of justice and exposes the sham credibility of Indian Courts" and added: "It also belies the rampant Indian duplicity and hypocrisy where India reflexively levels allegations of terrorism against Pakistan, while protecting with impunity terrorists who had publicly confessed to their odious crimes."

As per the press release, the acting foreign secretary said that Pakistan has previously raised the "lack of progress" as well as the "subsequent, concerted attempts by India to exonerate the perpetrators of this heinous terrorist act in which 44 innocent Pakistanis lost their lives".

It stated that the issue had been raised repeatedly at multiple occasions, including at the sidelines of the senior officials' meeting of the Heart of Asia in 2016. Additionally, formal demarches were also lodged with India with regards to the lack of progress as well as the acquittal of the accused in other cases.

The acting foreign secretary said that the "systemic Indian decision" to "gradually exonerate and finally acquit the perpetrators" was not just a reflection of India's "callous insensitivity" towards the families of the deceased Pakistanis but also "reflective of the Indian state policy of promoting and protecting Hindu terrorists".

As per the press release, he called upon India to explore "judicial remedies" in order to ensure that the perpetrators were brought to justice.