The changes are "responsive to the feedback" the MTA received, "which we believe will improve operations along the entire route," the spokesman said.
Adding the new stops will require building larger stops, installing new fare machines and adding new awnings and benches. The plan will also add an additional stop at Avenue L and Nostrand Avenue in Midwood, the spokesman said.
The MTA said it expects the service expansion to be completed early spring 2014.
B44 Select Bus Service began in November after about four years of planning and a year of construction, offering shorter travel times to bus commuters between Williamsburg, Bed-Stuy, Crown Heights, Flatbush, Midwood and Sheepshead Bay.
But after the program's launch, Bed-Stuy residents claimed that they were short-changed, with only two stops in the neighborhood at Lafayette Avenue and at Fulton Street, community board officials said.
"Everyone worked really hard to get this done," said Brooklyn Community Board 3 Chair Tremaine Wright. "We got the complaints, we passed [them] along, elected officials got on board— it was a community effort."
The new plan will also allow riders to transfer to the B52 at Gates Avenue and the B9 at Avenue L. Earlier this month, the MTA returned local bus service to the entire Nostrand Avenue line, whch was removed when Select Bus Service was put in place.