The federal agency that operates Brookhaven National Laboratory in Upton has agreed to increase its annual payment to Brookhaven Town by about 4 percent, officials said.

The Department of Energy has agreed to hike the contribution — known as a payment in lieu of taxes, or PILOT — by $55,000 to $1.397 million for the 2015-16 federal budget year, town and federal officials said. The town board is expected to approve the deal Thursday night.

The lab is exempt from paying property taxes because it is on federal land. The Energy Department agrees to make annual payments in lieu of taxes to the town, which distributes most of the funds to local school, fire and library districts and Suffolk County.

In a statement, Sen. Charles Schumer (D-New York) hailed the agreement as a “win” for taxpayers. Schumer previously has advocated for the lab’s PILOT payments to the town to remain stable and he criticized Energy officials in 2013 when it appeared the annual payment might not be increased.

“The Department of Energy’s renewed commitment to the residents of Brookhaven is both good news and the right thing to do,” Schumer said. “Local services, like fire districts and education programs, rely on this steady stream of PILOT payments to help keep essential services going and taxes in check. Town taxpayers deserve this win and I am glad the Department of Energy has heeded the call to keep the payments coming.”

The PILOT payment is meant to compensate the town and various taxing districts for income lost because of the lab’s tax-exempt status, officials said.

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“This is an annual process that recognizes the Department of Energy’s footprint on Long Island, through the presence of Brookhaven National Laboratory,” laboratory deputy site manager Robert Gordon said.

Town officials were not available to comment.

Negotiations between the town and federal officials went smoothly this year, without the hiccups that occasionally occurred in previous years.

In 2013, talks became tense when Brookhaven officials accused federal officials of planning to reduce the annual contribution and missing a deadline for making the payment. The federal government eventually increased the payment that year by $160,000.

Brookhaven officials plan to keep $125,000 of this year’s payment, town officials said. Those funds will be split up among general town expenses, the town highway fund, lighting districts, a clean water fund and the Manorville Ambulance District, which serves the lab.

The remaining money will go to school, library and fire districts in which the lab is located:

South Manor School District: $700,369.40

Longwood School District: 278,801.69

South Manor Library District: $34,650.37

Longwood Library District: $15,322.11

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Suffolk County: $180.988.95

Ridge Fire Department: $31,596.55

Manorville Fire Department: $30,801.55