The claim was immediately refuted by two ministers who said it was "wrong".
Raising the issue during Zero Hour in the Lok Sabha, Basheer said three women sarpanches from Kerala had gone to Gandhinagar to attend the Swachh Shakti 2017 - a Convention of Women Sarpanches which was addressed by Modi in Gandhinagar yesterday.
Women sarpanches from across the country had been invited for the event.
He said the women protested against the move and were let in on the condition that they would sit in the last row.
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"It took 45 minutes for these women to get into the venue. The PM should apologise to the nation," Basheer said.
Minority Affairs Minister Mukhtar Abbas Naqvi denied any such incident saying it is "contrary to facts" and the government does "differentiate anyone on the lines of caste, creed or religion."
Narendra Singh Tomar, Minister of Drinking Water, said the claim made by the MP has "no relation with reality. People are being misguided."
He said a women identified as Shalini Rajput did try to meet the Prime Minister by attempting to break the security cordon. She was stopped by the security personnel.