In a complaint, signed by more than 20 women parliamentarians, it was alleged that the Congress member made the "inappropriate gesture" towards Irani when was speaking in the House during the debate on the no-confidence motion against the government.
The minister for women and child development spoke after Gandhi, who alleged that the government's politics had "murdered Bharat Mata" in Manipur and termed members of the ruling BJP "traitors".
The Congress leader also slammed Prime Minister Narendra Modi for not visiting ethnic violence-hit Manipur and alleged that he does not consider the state to be a part of India.
BJP MP Irani said, "The person who spoke before me... an indecent gesture was made... only a misogynistic man can give a flying kiss to Parliament which seats female Members of Parliament... such indecent act has not been witnessed by the House ever before. The entire country has seen the culture of the (Gandhi) family."
Gandhi, while leaving the House after participating in the debate, was booed at by the treasury benches. He then turned around and a blew a flying kiss.
BJP MP and Union Minister Shobha Karandlaje, one of the signatories to the complaint, said that after "blowing a flying kiss towards Smriti Irani and all women members, he went away". "This is totally misbehaviour of the member. This is inappropriate and indecent behaviour of a member," she said.
"Senior members are telling this has never happened before in the history of Parliament... flying kiss is being given in Parliament. So, we have filed a complaint with the speaker to take the CCTV (camera) footage and take action against the MP," Karandlaje said.
Talking to reporters later, Irani said, "Never before has the misogynistic behaviour of a man been so visible in Parliament as what was been done by Rahul Gandhi today."
"When the House of the people, where laws are made to protect the dignity of women during the course of a session, stands witness to a man's misogyny, my question is should he not be brought to task," the Union minister said.
"We have heard that such indecent gestures are made on roads, we did not know misogyny is one of the traits of the Gandhi family," she said.
During her speech in the Lower House of Parliament, Irani also came down heavily on Gandhi for his "murder of India in Manipur" remark in Lok Sabha, saying this is for the first time in parliamentary democracy that someone has made such a statement. Manipur is an integral part of India, she said.