The Celebrity Big Brother winner was in tears when she was held at Mumbai Airport on her way to the opening of the Miss Bollywood musical in Germany.
Gere, 58, caused an outcry by grabbing Shetty, 32, and swept her backwards and kissed her at an Aids-awareness in New Delhi earlier this year.
The Pretty Woman star's effigy was burned in the streets of India's holiest city, Varanasi, after footage of him planting multiple kisses on Shetty's cheek was broadcast on Indian television.
The furore appeared to die down initially until a member of the public in the Rajasthani city of Jaipur filed a suit "in the public interest" alleging that Gere and Shetty had violated India's strict obscenity laws.
Such litigation is commonly used in India by individuals and special interest groups hoping to raise the profile of their causes or beliefs. The warrants are rarely enforced.
A judge issued warrants against Gere and Shetty after viewing video footage of the incident which, he said, "transgressed all limits of vulgarity and [had] the tendency to corrupt society."
The warrant was overturned by the supreme court but the immigration officials at Mumbai Airport had no record of the higher court's ruling.
They said Shetty was still wanted for obscenity charges over the kiss.
A person convicted of public obscenity faces up to three months in prison, a fine or both.
The star was only allowed to join the dance troupe performing with her at the Miss Bollywood musical after prolonged questioning.
Her spokesman, Dale Bhagwagar, said: "She called me in the middle of the night and was in tears."
Shetty said: "I can understand something like this if I'd committed a criminal offence.
"But what was my offence, when I'm just an actor, going to perform a musical on foreign land."
