The men provided logistical help to four LeT militants who carried out the attack that left eight people dead, IGP Munir Khan told the media.
The men, who had allegedly helped the four terrorists by providing them with vehicles and shelter, were arrested recently and taken into remand for further questioning, the police said.
The police said the four LeT militants, led by Abu Ismail, a Pakistani national, had attempted an attack on Amarnath pilgrims on July 9, but were frustrated by heavysecurity arrangements.
Another militant in the group of four had been identified as Yawar, a local recruiter for the LeT, the police said. Efforts are on to identify the other two, believed to be Pakistanis.
The police also released pictures of Abu Ismail and Yawar.
The the three "co-conspirators"-- Bilal Ahmed Reshi, Aizaj Wagey and Zahoor Ahmed --had carried out reconnaissance exercises and chosen Botengo near Khanbal as the spot where the attack could be carried out, the police added.
The trio had also provided shelter to the four militants in Khudwani and Sriguffwara of South Kashmir, Khan said.
Bilal's elder brother Adil, an alleged Lashker-e-Taiba terrorist, was killed by security forces earlier this year.
The Jammu and Kashmir Police had constituted an SIT led by Deputy Inspector General (South Kashmir) Swayam Prakash Pani to probe the attack on the pilgrims.
Eight people were killed when the militants fired at a bus carrying the pilgrims, returning from their Amarnath yatra. It was the biggest militant attack on Amarnath pilgrims after the insurgents killed 30 yatris in Pahalgam in the year 2000.
Showing exemplary courage and presence of mind while driving through the bullets, Sheikh Salim Gafoor, the driver of the bus had saved lives of over 50 pilgrims.
After the Salim told had reporters that God gave him the strength to keep driving despite the firing.
"Firing was going on from all sides, so I kept driving and did not stop," he said. "God gave me the strength to keep moving... I just did not stop anywhere."