Suffolk will hand out $1 million in bonuses to its employees as part of a spending plan for a $4.1 million surplus.

Suffolk Public Schools also will receive a total of $1.68 million from the pot to hand out to its employees in bonuses.

The bonuses will equal 2 percent of each employee’s annual salary. City Council passed the measure unanimously Wednesday night.

In discussing the proposal, Budget and Strategic Planning director Anne Seward noted that employees had not received a raise since July 2008 and a recent study found Suffolk employees’ salary was roughly 9 percent less than their counterparts in comparable cities.

“I think what we’re doing tonight is the right thing,” Mayor Linda T. Johnson said just before the vote. “The buildings are only as good as the people inside.”

The remainder of the surplus, about $1.4 million, will be placed in a capital contingency fund.

The unexpected windfall came from a surge in meals, business license and sales taxes, Seward said. New businesses in the city that opened in recent months, such as T.J. Maxx and PetSmart, were partly responsible, she said.

Councilman Robert Barclay said ensuring city staff remains “competent and motivated” is one aspect of being good stewards of the taxpayers’ dollars.

Both he and Councilman Michael Duman said they initially leaned toward providing a flat-rate bonus but decided it would be unfair to reward new employees the same as workers who have been around for decades.

“Your pay is not just a function of your position, it’s also a function of your time and service,” Barclay said.

The bonuses include all school positions and city positions, including grant-funded positions, City Council appointees, court employees and constitutional officers.

Seward indicated the ratings agencies had been disappointed to hear, during recent meetings, that the city would not provide raises this year but had been happy to hear that bonuses might be provided.

Councilman Leroy Bennett said he hoped the move would demonstrate that the city cares about its employees.

“We are trying to do the right thing,” he said.