Suffolk County is making a last-minute push to get state lawmakers to clarify its farmland protection program, which a dozen farmers said Tuesday has been in “disarray” since a September court decision struck down the county’s permitting process for structures on protected land.

The Suffolk Legislature passed a home rule message 17 to 0 to support Assembly and Senate bills introduced by Assemb. Fred Thiele (I-Southampton) and Sen. Kenneth LaValle (R-Port Jefferson). The law says protected farmland shall be allowed to build structures for “farm operations,” as defined by the state agriculture and markets law. The State Legislative session ends June 21.

Thiele said the bill “will remove uncertainty” so the county could start issuing permits.

But he pegged the bill’s chances as “uncertain” because the State Legislature typically doesn’t act when a matter is under litigation.

Suffolk County has appealed the decision by State Supreme Court Justice Thomas Whelan that nullified 2010 and 2013 amendments to the county’s farmland protection program.

Karl Novak, a farmer in Laurel and president of the Long Island Farm Bureau, said the court decision has “thrown the county farmland preservation program into total disarray.”

The county has stopped issuing permits for irrigation wells, deer fencing and barns on protected farm lands. Also, the uncertainty with the program’s future has halted sales of farmland development rights and financing based on the land, Novak told lawmakers.

Dick Amper, executive director of the Pine Barrens Society, which sued the county and farmland committee, said the lawsuit never intended to block deer fencing or irrigation. But the county had allowed too many permanent structures, including greenhouses, on land purchased with the proceeds from a voter-approved sales tax referendum.

He said in a phone interview the county should take any changes it wants to make to voters.

“All the county legislature has to do, if it wants to allow more development on [protected] farmland, is put it in front of the voters at referendum,” Amper said.

Suffolk has spent $260.8 million to preserve 10,636 acres of farmland.

In other action, county lawmakers directed the county attorney to explore suing the Long Island Power Authority for allegedly underpaying $6.6 million in tax payments. Comptroller John Kennedy, who is backing the proposal, said the underpayment could rise to more than $10 million with the current year’s taxes.

The dispute involves when LIPA started applying a state-approved 2 percent cap to property tax payments and whether the authority could pay apply the cap based on individual parcels, or in the aggregate.

In a statement, LIPA outside counsel Don Leistman said LIPA received bills from some Suffolk towns that incorrectly exceeded the 2 percent cap enacted in 2013. “Comptroller Kennedy should work with the Suffolk towns to fix the billing system as happened in Nassau County,” Leistman said.

Lawmakers also approved a capital budget with $94.3 million in serial bonds in 2018. The amount is $1.4 million less than the budget submitted by Bellone and $20.5 million lower than what was approved in 2017. Democrats defeated a Republican proposal that would have cut 11 percent from most projects. Republicans said the county is broke and needed to start spending less. Democrats called the cuts arbitrary.

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