A statement from the Indian Ministry of External Affairs on Saturday said the fee would have humanitarian consequences "by way of the disruption caused for families".
The Indian government "hopes that these disruptions can be addressed suitably by the US authorities", it also said.
The exchange of skilled workers has "contributed enormously" to both nations, the statement said, adding: "Policy makers will therefore assess recent steps taking into account mutual benefits, which include strong people-to-people ties between the two countries."