The Metropolitan Transportation Authority agreed to change the flashing blue lights on its Select Bus Service.
The decision comes months after local elected officials raised concerns that the lights were causing confusion among drivers.
The lights on the select buses alert riders that their bus is approaching.
In September, City Councilman Vincent Ignizio and state Sen. Andrew Lanza wrote a letter to the MTA asking it to discontinue the use of blue flashing lights on the buses.
They say a state law prohibits such lights on non-emergency vehicles.
Some Islanders say it has caused them to unnecessarily pull over because they thought an emergency vehicle was approaching.
A spokeswoman for the MTA said the agency is still working out the details, but changes will be made over the next few months.