An Indian court Wednesday handed down a rare guilty verdict against three Hindu radicals over a shrine bombing, but cleared the alleged mastermind of the attack initially blamed on Islamist groups.

Devendra Gupta and Bhavesh Patel were convicted in a special court in Rajasthan over their roles in the 2007 bombing of the Ajmer Sharif dargah.

A third man, who was shot dead in the months after the attack, was found guilty posthumously.

The trio was convicted of charges related to explosives and conspiracy to commit unlawful acts over the strike that left three dead and at least 15 injured, the men's lawyer Jagdish Rana told reporters outside the Jaipur court.

Their sentences will be handed down on March 16.

Naba Kumar Sarkar, the alleged ringleader behind the religiously motivated attack, was among seven Hindu radicals acquitted after prosecutors failed to prove their guilt.

Sarkar, better known by his nickname Swami 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.

The landmark judgement against the trio over the shrine bombing is the first successful conviction of Hindu militants in recent memory.

Police initially blamed Pakistan-based militants for the attack on the revered 12th-century mausoleum, claiming they placed the lunchbox packed with explosives that detonated during Ramazan prayers.

But a confession by Sarkar led investigators to a group accused of staging a series of blasts targeting Muslims.

Sarkar later retracted his confession but police were able to sweep up suspected radicals, including a serving Indian army officer and former members of Rashtriya Swayamsevak Sangh.

The prominent right-wing Hindu group bears considerable influence in India, and is the ideological fountainhead of Indian Prime Minister Narendra Modi's ruling nationalist Bharatiya Janata Party.