Everyone give their own theory when asked about how these incidents can stop and who is responsible for them. Some blame women for these incidents and some blame men for the same.
Mr Khan, 49, was in the city to speak at the prestigious sixth annual 'Women in the World' summit presented by renowned journalist and author Tina Brown in association with the New York Times.
"Rape is a big issue in India," Mr Khan said in a session titled Tackling India's Taboos.
He was in conversation with Iraqi-American humanitarian Zainab Salbi, who founded Women for Women International, a grassroots humanitarian and development organisation dedicated to serving women survivors of war.
The PK star said a rape survivor was often ill-treated by police and medical staff and did not get swift justice.
"The balance of power in India needs to change. Unless conviction becomes swift and certain, things are not going to change in India. And very importantly, as a society we have to shun the rapist and hold the survivor close," Mr Khan said to a huge round of applause from the audience.
The audience included Oscar-winning actress Meryl Streep, talk show host Jon Stewart and designer Diane von Furstenberg. When asked about the ban on the documentary India's Daughter in the country, Mr Khan said it was "unfortunate" that the film was not shown in the country.
While Mr Khan said he had not seen the film yet, he added that the documentary should be shown in India and 'there should be freedom of speech everywhere.'
The Bollywood actor also stressed on the need to begin gender sensitisation of children, especially boys, at an early age, saying that society should let young boys know that it is alright for them to cry, feel scared and express their emotions.
"Is a real man someone who goes and beats up people, is a real man a person who is the protector. Unless we re-look at and hopefully re-define what a man is, things are not going to change," he said amid a huge round of applause from the audience.
He said it is not correct for parents and society to tell young boys not to cry since such an attitude will make the boys insensitive.
"A boy grows up feeling that I'm not supposed to cry. When you tell a child not to cry, you are removing him further and further away from his emotions. And then you are surprised why he is beating up his wife."
He added that from his conversations with people in India, a real man is defined as one who doesn't cry, doesn't hold his wife's hand and doesn't hug his children.
"Based on all of these definitions of what a real man is, I'm completely not a real man because I hold my wife's hand all the time, hug my children and I cry all the time," Mr Khan said.
Dressed in a blue jeans and jacket, the actor also spoke about his upcoming film Dangal and admitted that he had put on weight for his role in the film. He plays a wrestler who wishes, to win a gold medal for his country and whose dream is eventually fulfilled by one of his four daughters.
The audience was also shown clippings from Satyamev Jayate, Mr Khan's show which dealt with social evils like female foeticide, dowry, child sexual abuse, rape and inequality. The actor said that the popularity of the show indicated that 'India wants to change, India is ready for change.'
Aamir Khan said, "The fact that (the show) is so popular really speaks well for us as Indians today, that we have issues, we have problems but we want to leave them behind, we want to come out of them and we really want to go ahead and improve ourselves."
He revealed that in his five years on Satyamev Jayate, he had seen 'the worst and best of mankind'.
(With inputs from agencies)