Some airlines have already been hit by measures to discourage people from travelling from Saudi Arabia to Bahrain to catch international flights.
They expect their load factors to decrease further if more measures are implemented.
The Saudi Presidency of Civil Aviation (SPCA) has ordered foreign airlines to stop issuing boarding passes and checking baggage in the Eastern Province for Bahrain International Airport (BIA) -bound airline passengers crossing the King Fahad Causeway.
A Bahrain Civil Aviation Affairs official said that talks were underway with the SPCA about the moves.
Saudi Transportation Ministry officials were unavailable for comment.
Airline representatives say the practice, which has gone on for years, has been a customer convenience that streamlines check-in procedures.
While airline executives have expressed their disappointment with the initiative, they all say they will comply with the directive.
However, they say they will do what they can to persuade the Saudi Arabian Government to reconsider the move.
"The situation is volatile and very sensitive right now," said Gulf Air public relations manager Ahmed Al Janahi.
"But I don't think it should be blown out of proportion."
It will have an adverse effect on Bahrain's aviation industry, he said.
"However, it will not be as devastating as people are envisioning," he added.
"Gulf nationals will still maintain their right to travel freely across the causeway no matter what their reason."
People with valid visas will still be able to travel, added British Airways sales manager (Eastern Province) Richard Hirsch.
"The only disruption will be the check-in inconveniences," he said.
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