The first two phases of the Fairfield Ludlowe High School renovation/expansion project will be ready when students return in September, the Board of Selectmen was told Wednesday.

But replacement of windows and remediation of PCBs found in the caulking, which had triggered the project five years ago, won’t be done until 2016 because there is not enough money in the $11.6 million budget.

Prior estimates pegged the window replacement at $3 million, with another $750,000 for remediation.

The first phase, which included replacing 80 percent of the building’s roof, had to be rebid and caused a four-month delay. Meanwhile, bidding for the second phase — construction of the classroom and cafeteria addition — was put off for several months because of delays in plan approvals. Those factors, building committee Chairman Marc Donald told the selectmen, contributed to the project’s increased costs. Another reason, he said, was the accelerated construction schedule.

While there is enough money in the budget to cover those phases, the committee plans to go out to bid for the window replacement and remediation before returning to town boards for additional funding. That work would be done in the summers of 2016 and 2017.

The selectmen appeared to understand the reasons for the project’s increased cost, but were not pleased to learn that those higher costs will bump up the payment to the architect for the project, Perkins Eastman.

The firm’s fee is based on 5.5 percent of the total project cost. That type of payment structure, Selectman Sheila Marmion said, is a disincentive to get the project completed on time and under budget.

The firm will be paid more, First Selectman Michael Tetreau said, even though it has not done any additional work.

“The project costs more because we accelerated the schedule, but the architect didn’t spend any more hours on it or incur anymore costs,” Tetreau said.

Marmion said that kind of contract provision is something officials need to review in regard to future projects.