Judge Dinesh Gupta issued the warrants in the northwestern city of Jaipur after a local citizen filed a complaint charging that the public display of affection offended local sensibilities, the Press Trust of India news agency reported.
Gupta earlier viewed television footage of the event, which he called "highly sexually erotic," saying the pair violated India's strict public obscenity laws.
Gere and Shetty "transgressed all limits of vulgarity and have the tendency to corrupt the society," PTI quoted the judge as saying.
Such cases against celebrities - often filed by publicity seekers - are common in conservative India. They add to a backlog of legal cases that has nearly crippled the country's judicial system.
Gere left India shortly after the kissing incident and it was not immediately clear how the warrant would affect him.
Gere is a frequent visitor to India, promoting health issues and the cause of Tibetan exiles. The Tibetan spiritual leader, the Dalai Lama, has his headquarters in the northern Indian town of Dharmsala.
Under Indian law a person convicted of public obscenity faces up to three months in prison, a fine, or both.
Last week, crowds in several Indian cities burned effigies of the 57-year-old star of "An Officer and a Gentleman," "American Gigolo" and "Pretty Woman" after he embraced Shetty and kissed her several times on her cheeks during an HIV/AIDS awareness event in the Indian capital.
Photographs of the clinch were then splashed across front pages in India, where public displays of affection are largely taboo.
The judge lambasted Shetty for not resisting Gere's kisses and ordered her to appear in his court May 5, PTI said.
Shetty, who is currently on a religious pilgrimage in southern India, was upset by the news, her spokesman, Dale Bhagwagar, said.
"She does hurt, she does feel low," Bhagwagar told The Associated Press. "She feels she is being constantly targeted, but anyone who knows her well knows she can't be put down."
"Shilpa wishes that people would focus on the real issue , AIDS awareness, and not three pecks on her cheek," he said, adding that she had not yet received any court summons.
Shetty, already well known in India, became an international star after her appearance on the British reality show "Celebrity Big Brother" - another controversial public appearance. A fellow contestant, Jade Goody, sparked international headlines by making allegedly racist comments to Shetty. Mobs took to the streets of India to denounce Goody, and Shetty went on to win the competition.
"As soon as we can see the concentration of American aircraft on airfields in Europe, we will simply destroy those airfields by launching our medium-range ballistic missiles at those targets"