Rahul made the claim at a poll rally in Indore in Madhya Pradesh while accusing BJP of creating a divide in Samajwadi Party-ruled Uttar Pradesh for political gains.
Slamming the Congress Vice President for his claim, BJP interpreted it as an attempt to cast doubts about the patriotism of Muslims and demanded that he tender an apology.
The UP police said it had no information about the claim but would verify it.
He said he had been told by an intelligence official that as a consequence of the alleged communalisation in Muzaffarnagar, there was a group of 10-15 Muslim youngsters, whose kin were killed, with whom intelligence agencies of Pakistan have established contact.
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Rahul claimed that the official told him he was convincing the youngsters not to come under the influence of Pakistani operatives.
"Gandhi has raised questions about the patriotism of Indian Muslims by saying they were approached by ISI. This is unfortunate. He should apologise for his remarks," said Hussain, the right-wing party's Muslim face.
Hussain said BJP has never said Indian Muslims are communal or that they can be influenced by Pakistan's ISI.
The UP police denied having any information about Pakistani intelligence agencies being in touch with Muslim youths in riot-hit Muzaffarnagar as part of their sinister designs.