Special court judge Pradip Sawaikar acquitted all the accused for want of enough evidence against them.
Two accused - Malgonda Patil and Yogesh Naik - who were ferrying the explosives to a crowded spot in Margao town where the low intensity blast occurred on October 16, 2009, were killed in the explosion.
The explosives went off a few metres away from the targeted site when the two were commuting on a scooter. Apart from Patil and Naik, no other casualty had occurred in the blast.
Later, the investigation was transferred from Goa crime branch to the National Investigation Agency (NIA), which had filed the charge sheet in the case on May 17, 2010.
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The NIA in its charge sheet had claimed that four more accused were absconding.
The blast had pointed fingers towards a right wing Hindu organisation, Sanatan Sanstha, which is headquartered at Ramnathi village in Goa.
Malgonda Patil, who was allegedly ferrying the explosives, was connected to the organisation.