Under previous rules, tourists on five or 10-year visas were required to leave the country every 180 days.
But many would simply fly to a neighbouring country such as Nepal for a brief stay before returning.
Now they will still face the same 180-day deadline, but will have to stay out of the country for two months before they can re-enter.
"We have changed the rules to prevent the misuse of the long-term tourist visa," a senior official at the foreign ministry told AFP, asking not be named.
The new rules have been implemented since November 4, he said, although the British and the US embassies in New Delhi said the changes were being applied inconsistently and had caused problems for a number of its nationals.
In a posting on its website, the US embassy detailed a number of tourists who had left the country to visit a neighbouring country for a holiday but who were then denied entry back into India.
"These new visa and registration regulations are being implemented incons