Two Long Island public school districts, Hempstead and Wyandanch, faced the highest degree of fiscal stress encountered by any non-urban districts in the state, the comptroller’s office reported on Wednesday.

State Comptroller Thomas P. DiNapoli, in his annual report on schools’ financial condition, said that the total number of districts either in financial stress or at risk of difficulties declined during the past year, both statewide and on Long Island.

Overall, 59 districts statewide, including 18 in Nassau and Suffolk counties, encountered some degree of fiscal difficulty during the 2015-16 school year, according to the report. Those numbers were down from 82 districts statewide and 25 districts in the region the year before.

“Fiscal stress in many school districts has declined, especially for those in the most severe condition,” DiNapoli said. “School officials should be commended for working to keep their districts out of financial harm, but should be careful not to amass excessive levels of fund balance in order to do so.”

On the Island, some education advocates said the report’s spotlight on Hempstead and Wyandanch underlined a crucial point: The Island’s school systems, while generally middle-class or affluent, include a number of districts with high concentrations of poverty.

In Wyandanch, for example, 87 percent of students qualify for subsidized lunches because of modest or low family incomes, while in Hempstead that figure is 75 percent. The statewide average is 52 percent, according to state Education Department data.

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“This is definitely a problem on Long Island,” said Blanca Villanueva, Long Island education organizer for the Alliance for Quality Education, a statewide organization that focuses on issues faced by high-need districts. “We have districts that are highly segregated, and this includes Hempstead and Wyandanch. These are schools that are struggling. These are schools that are owed millions of dollars in state aid.”

The question of just how much financial assistance will go to public schools in 2017-18 is under debate in Albany, where Gov. Andrew M. Cuomo last week proposed a $1 billion, 4 percent increase statewide in operating aid to local districts.

DiNapoli’s report, “School Districts in Stress,” attempts to measure districts’ financial condition through a formula based on several indicators: short-term borrowing, year-end fund balance and patterns of operating deficits.

The comptroller’s office, which has issued the report for four consecutive years, identifies schools in three categories. Hempstead and Wyandanch are rated as being in “significant stress,” the category of greatest difficulty.

Hempstead and Wyandanch officials agreed that their districts were struggling, but managing to improve nonetheless.

Wyandanch’s superintendent, Mary Jones, said her district spent $1.5 million on portable classrooms two weeks ago to help accommodate hundreds of students recently arrived from Central American countries, who crossed the United States’ border with Mexico as unaccompanied minors and were resettled here with parents or sponsors while their immigration cases are pending.

Jones added that her district is making progress in stabilizing its finances, as did Maribel Touré, president of Hempstead’s school board.

“Yes, we’re having a lot of financial stress, but I think this year we did much better, being financially responsible while also providing better educations,” Touré said.

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Amityville and another eight districts statewide were designated as being in “moderate stress.”

Mary Kelly, the Amityville superintendent, said a local decrease in fund balance was due to a one-time retirement incentive for teachers, and that the district was working to build reserves and fund balance.

Forty-eight districts, including 15 on the Island, are “susceptible to fiscal stress,” the category of least difficulty.

Vincent Butera, the Bayport-Blue Point superintendent, said the district could be removed from the list as soon as next year, as it reduces expenses and improves efficiency. Ken Bossert, Elwood’s school chief, said his district’s finances are on a “positive trajectory” and would improve further.

The comptroller’s rating formula has drawn complaints over the years from some district administrators, who say it does not take special circumstances into account. Jericho was placed on the latest “susceptible to fiscal stress” list, even though its taxable wealth is more than double the state average.

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The comptroller’s office said that Jericho appeared to have a large budget deficit last year. But Hank Grishman, the district superintendent, said that his system simply had shifted funds from its operating budget to a capital reserve fund.

“On the record, I want to make clear that Jericho is on a very sound footing, and that there are significant flaws in the comptroller’s formula,” Grishman said.