The issue was raised in the Rajya Sabha by Leader of the Opposition Ghulam Nabi Azad.
Azad said a question mark had been placed on the dignity of the prime minister.
He also demanded Prime Minister Modi's presence to explain the allegations.
Media reports said Tuesday that Manmohan had met Naidu personally and told him about the allegations.
Modi had, while campaigning in Gujarat, said Manmohan Singh, former Congress leader Mani Shankar Aiyar, and former vice-president Hamid Ansari had met with the Pakistani high commissioner and former foreign minister Khurshid Mahmud Kasuri and discussed the Gujarat elections.