The National Investigation Agency (NIA) on Monday cleared four people, including Sadhvi Pragya Singh Thakur and senior Rashtriya Swayamsevak Sangh (RSS) leader Indresh Kumar, of charges in the 2007 Ajmer Dargah blast case.
Earlier in the day, a report was submitted in the special NIA court in Jaipur as the counter-terrorism agency could not find enough evidence against the four.
Three more accused Sandeep Dange, Suresh Nair and Ram Chandra Kalsangra are still held responsible for the crime.
Justice Dinesh Gupta expressed disapproval over NIA's inability to arrest the trio.
The court has written to NIA's Director General of police (DGP), asking for a progress report on efforts to arrest the other three.
The explosion at the popular Sufi shrine in Ajmer in October 2007 killed three people and wounded 17.
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Besides Ajmer, Sadhvi has been a suspect in the 2008 Malegaon bombing that killed seven people.
The special NIA court had earlier found Hindu right-wing activists Sunil Joshi and Devendra Gupta guilty of planning the blast, and Bhavesh Bhai Patel of planting the explosive.
Both the men were sentenced to life imprisonment on March 22.
Earlier this week, the court had directed the NIA to present evidence that verifies the deaths of two other people in the case, Jayanti Bhai Gohil and Ramesh Gohil. Both men were accused in the Gujarat Best Bakery Blast in 2002.