There appears to be no respite for the National Investigation Agency as more and more witnesses turn hostile in terror cases allegedly involving Hindu extremists ever since the National Democratic Alliance government took over last year.

A spate of terrorist attacks, targeted at Muslims in India, had taken place during 2006-2007. These included the Malegaon blast of 2006, the Mecca Masjid blast in Hyderabad in 2007 and the Samjhauta Express blast in 2007. The names of organisations such as the Rashtriya Jagran Manch, Sharda Sarvagya Peeth, Hindu Rashtra Sena and Abhinav Bharat had come up during investigations and some of the people linked to these organisations were arrested. There were several common accused in these cases of terrorism and the BJP and the Shiv Sena had charged the investigating agencies of having political motives behind the arrests.

Reports have now emerged that the cases, where the accused are Hindu extremists or belonged to the organisations close to the Bharatiya Janata Party and the Rashtriya Swayamsevak Sangh, have been considerably weakened with key witnesses turning hostile. The spate of U-turns by witnesses in these cases in recent months has led to speculation that these were linked to the shift of power at the centre in May 2014.

This has also lent credence to the claim by Rohini Salian, the NIA's special public prosecutor in the 2006 Malegaon blast case, that she was asked to "go soft'' in the case after the new government took over.

So far 15 prosecution witnesses in the 2007 Samjhauta Express blast case and 19 witnesses in the Ajmer blasts case have turned hostile over the last few months and there are reports that several more are likely to go back on their earlier statements. Most of these statements were given before a magistrate under Section 164 of the Code of Criminal Procedure. The relevant section states that the “Magistrate shall not record any such confession unless, upon questioning the person making it, he has reason to believe that it is being made voluntarily”. Such statements are admissible in courts unlike those recorded by police or investigating agencies.

Samjhauta Express blast case
The blast in the Attari bound Samjhauta Express had taken place on February 18, 2007, near Dewana railway station in Panipat district, killing 68 passengers and injuring 12. Most of the victims were from Pakistan and the blast had provided a major setback to India-Pakistan relations. Even now, Pakistan rakes up the issue of slow progress in prosecuting those responsible for the blast each time India takes up the issue of Mumbai blast accused residing in Pakistan. Swami Aseemanand, believed to be close to the Sangh Parivar, is one of the main accused and is in the custody of the NIA.

Two of the prosecution witnesses who resiled from their statements earlier this month had earlier stated that the prime accused Aseemanand had made extra-judicial confession before them that he was involved in planning and execution of the blast. One of them, Ajay Chauhan, a resident of Haridwar, had given a statement to the NIA, in the presence of a tehsil official, that Aseemanand had told them that his associate in the blast, Sunil Joshi, had been murdered to ensure that the police does not question him and that the investigating agencies were also on the lookout for him. Another witnesses, who had earlier stated that he was aware of a conspiracy hatched by Aseemanand and Pragya Singh Thakur, also went back on his statement.

The NIA had listed 299 witnesses in the case, out of which 145 have been examined so far and 15 have turned hostile. These include Bharat Bhai, his wife Kavita, Shivam Dhakad, Ram Charan Patel, Sheetal Gahlot, Rohit Kumar, Jagdish bhai, Ghanshyam Magharam and Neera.

The NIA prosecutors don't deny that so many witnesses turning hostile would have a negative effect, particularly when the case rests only on circumstantial evidence. Advocates for the witnesses, however, point out that confessional statement were extracted from them by the then Congress government to frame the BJP and the Sangh Parivar.

Ajmer blast case
There are even more serious consequences for the Ajmer blast case as it has been considerably weakened by witnesses turning hostile. There were only 15 accused who had recorded their statement under Section 164 and 14 of them have now turned hostile. All these 14 witnesses were key witnesses while a large number of the remaining witnesses were the injured persons or police officers who are not key witnesses.

Among the key witnesses who have resiled is Randhir Singh who had defected to the BJP from Jharkand Vikas Morcha (Prajatantrik) and is now a minister in the Jharkand government. He told the court in May this year that the Anti Terrorism Squad had "pressurised'" him to make the statement. The quid pro quo in the case is quite obvious.

Three persons were killed and 17 were injured in the Ajmer dargah blast in 2007. The case was handed over to the NIA in 2011.

It had raked up considerable controversy when Indresh Kumar, National Executive Council member of the RSS, was among those chargesheeted. Several other accused including Aseemanand and Sadhvi Pragya figure in both Samjhauta and Ajmer chargesheets.

Malegaon cases
The controversy over the investigations in the Malegaon cases is the latest in the series. The blasts had taken place on September 29, 2008 near Bhikku Chowk in Malegaon. Almost simultaneously a blast had taken place at Modasa in Gujarat on the eve of Navratri. Four people were killed in Malegaon, while a boy lost his life in Modasa. Two low intensity bombs were fitted on a motorcycle which later led the police to the accused.

Initially, the suspects were believed to be Muslim extremists but following the trail of the motorcycle, the ATS collected evidence which pointed to the involvement of Hindu extremist groups behind the blast. Sadhvi Pragya Singh Thakur, Shiv Narayan Gopal Singh Kalsanghra and Shyam Bhawarlal Sahu were later arrested in connection with the blast.

As the controversy over the allegations of complicity between the prosecution and the accused in the Malegaon blast case of 2008 reached the Supreme Court and it sought replies from the home ministry and the NIA.

The NIA has responded by telling the court that none of the accused have been granted bail since June 2014 when Salian was allegedly asked to “go soft” – a charged it called "unwarranted and baseless” – and that all the accused who managed to be let off on bail was during the time Salian represented the NIA.

In its reply to the court, the NIA also pointed out that it had nothing to gain by trying to influence Salian since all matters related to the Malegaon blasts cases were before the apex court during June 2014 and Salian "was appointed as Special Public Prosecutor for the NIA only within Maharashtra and therefore, there was no way anyone within or outside NIA would have gained by asking her to go soft".

Earlier, the NIA told the home ministry that it had recommended removal of Rohini Salian as its special public prosecutor because she wanted the agency to file an application in court to discharge nine Muslim men initially arrested in the earlier, the 2006 blast case in Malegaon. When it refused to comply, the NIA alleged, Salian refused to file the chargesheet in the case.

Salian has denied NIA’s allegations. “The investigation officer’s report in the 2006 Malegaon case held that the first investigation (conducted by Maharashtra ATS) was wrong and that NIA’s was right. Based on this, I recommended that justice must be done to the Muslim men. Initially, the officers who I discussed the issue with agreed. I do not know what instructions flowed from the top brass later, they refused to file a discharge application,” she told the Indian Express.