Beniwal had levelled corruption charges on the state revenue minister Harish Choudhary because of which he faced the wrath of Congress workers.
No one was injured in the incident but window panes of the minister's vehicle and a police jeep were damaged, police said.
Beniwal and Union minister Kailash Choudhary were scheduled to attend a religious function at a temple in Baytoo area of Barmer at night. When they reached there, some of the Congress workers pelted stones at the vehicle, police said.
Baytoo is the assembly constituency of the state revenue minister Harish Choudhary.
"There was resentment among the Congress workers. They assembled near Baytoo last night saying they will not let the MP attend the function.
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"They were initially pacified. Senior police officers were also present but when the vehicles arrived, some of the Congress workers pelted stones at the vehicle of the union minister in which RLP MP Hanuman Beniwal was also present," SP Barmer Sharad Chowdhary said.
He said the situation was brought under control and both the leaders attended the function amid police security.
After the function was over, the minister stayed at Balotara town in Barmer while the RLP MP from Nagaur was escorted by the police to the Jodhpur border.
Efforts are being made to arrest the accused, he added.
Hanuman Beniwal's RLP is an NDA alliance partner. He had contested and won the Lok Sabha election from the Nagaur seat as the alliance candidate last year while BJP's Kailash Choudhary represents Barmer constituency in the Lok Sabha.
(With additional information from PTI)