The actor featured the issue on an episode of his well-received discussion show Satyamev Jayate.
He told The Times of India: "I think female foeticide is a very serious issue. And if it continues the way it is, it will get worse. I am so happy that Maharashtra government is likely to propose this (severe punishment).
"I want to add here that abortion is legal and it should be. I am pro-choice for women. But female foeticide, when we find out the sex and kill the girl child, should finish and very severe punishment should be given."
The producer and television host added: "I am happy that people are connecting emotionally with the show. My team and I like that we have reached people's hearts and have churned ideas.
"There are so many things which are hidden and they need to be brought out in the public light. These things need to be discussed so that they can be dealt with."
It is calculated that there are 914 girls to every 1,000 males in the country because of female foeticide rates, according to the paper.
In May, Khan successfully asked Parliament to pass a bill to protect children against sexual exploitation after debating the issue on his programme.
The 3 Idiots star has previously raised awareness of malnutrition in the country.