But the testimonies of three eyewitnesses who claim to have survived the massacre, have blasted holes in that theory.
Now, in their first ever TV interview, the three men spoke to NDTV from a safehouse in Madurai, describing in detail how the police allegedly abducted their friends and family as they entered Andhra Pradesh.
The most chilling is the testimony of 20-year-old Ilangovan, who left his impoverished village in Tiruvannamalai district in Tamil Nadu in a bus along with a friend, Paneerselvan. He thought he was being taken to do coolie (manual labour) work.
But, he alleges, when they stopped at night for a snack of pani-puri in the town of Nagari Puttur, just across the border in Andhra Pradesh, they were surrounded by the police.
He says they tried to get into an autorickshaw, but were intercepted by the police. Soon, he says, a truck arrived, and they were thrown into the back of it. The police did not explain why, says Ilangovan.
The vehicle, he says, had 20 people in it, and was driven to a place with lots of trees and police vehicles.
According to human rights activist Henri Tiphagne, who is representing the witnesses at the National Human Rights Commission, the place described by Ilangovan closely resembles the headquarters of the Anti-Red Sanders Smuggling Task Force in Tirupati, not far from where the encounter took place.
Ilangovan says at this location, they were asked to come down from the truck, and their photos were clicked by the police.
Ilangovan's account mirrors that of another witness, Balachandran, who alleges that an agent named Palani arranged for a group of eight people from their village in Dharmapuri in north Tamil Nadu, to travel to Andhra Pradesh for masonry work.
His father Harikrishna was part of the group. They, too, were brought to the town of Nagari Puttur. Balachandran and Palani's associate stopped for a drink at a local liquor shop, while his father and the others went ahead.
Suddenly, he says, he got a call saying the group had been arrested and brought to Tirupati.
When he called back, a stranger picked up the phone, asking them to join them. But, sensing something was wrong, Balachandran returned home. Two days later, his father's body arrived in the village, riddled with bullets.
The third eyewitness Sekar, who was travelling from Tiruvannamalai says that when they crossed into Andhra Pradesh, an unidentified man boarded the bus and forced three men from his village to disembark. This included his friend Mahendran. Sekar turned back immediately. The next he saw Mahendran was when his body returned to the village.
We asked them why they have chosen to speak out, given the risks involved. "We are speaking out for justice for the 20 killed," said Sekar.