Hardeep Singh filed a complaint with the police over the attack.
Another witness in Uttar Pradesh's Lakhimpur Kheri case, in which the son of a Union Minister is accused of running over farmers, has alleged that he was attacked and threatened not to testify.
Hardeep Singh said he was attacked by a group of people on Sunday in the Rampur district over his role as a witness in the case involving Ashish Mishra, the son of Union Minister Ajay Mishra Teni, who is the member of parliament from Lakhimpur.
"I was returning after praying at the gurdwara. A car came from the back with three-four people. Another car had three-four more. The stopped me. One of them started to beat me. Another hit me from behind. I was hit with a kadha and the butt of a pistol. They said, 'If you go to testify, we will shoot you'," Mr Singh said.
He named Mehar Singh Dayol, a local leader of the BJP in Rampur, and Saranbjeet Singh.
The police, however, contested the charge, saying they had not found any link to the Lakhimpur Kheri case in which Mr Mishra is accused of running over farmers with an SUV during a protest march in Lakhimpur Kheri last year.
"Based on a complaint by Hardeep Singh, son of Hari Singh, an investigation by officers and eyewitness testimony, the incident prima facie appears to be one of road rage. So far, we have not found any link to the Lakhimpur violence. Action is being taken against the three accused named in the case and others," the police said in a statement in Hindi.
Mr Singh is the second witness in the Lakhimpur Kheri case to allege an attack on him. A witness was attacked in March and attackers had issued threats citing the BJP's victory in the recent UP election, farmers groups had alleged, saying Ashish Mishra's bail must be cancelled as he is a threat to witnesses.
Eight people died in Lakhimpur Kheri on October 3. After four farmers and a journalist were crushed by the convoy of the Union Minister's son, three more, including BJP workers, were killed in violence that broke out later.
The Supreme Court, which is hearing the petition to cancel Mr Mishra's bail, had asked the state government to ensure the safety of witnesses.