When officials of the Town of Lockport Industrial Development Agency received the word that the state plans to charge a fee for “cost recovery of central government services,” they thought it might be a joke.

“Is this a serious communication?” Alan Hamilton, the agency’s board chairman, asked after the letter, billing the agency $926, was read at a meeting this month.

But it’s not an episode of “Albany’s Funniest Practical Jokes.” And the Niagara County IDA, which is being billed $219,349, really isn’t laughing.

“Incomprehensible,” said Henry M. Sloma, chairman of the Niagara County agency’s board. “I thought the people of Niagara County were paying for the cost of central government through their taxes.”

Alfred Culliton, the chief operating officer at the Erie County Industrial Development Agency, isn’t amused either. That agency faces a $225,000 bill as a result of the new assessment on industrial development agencies.

“It’s crazy because you’re taxing the very activity that you expect will create jobs,” Culliton said. “The state’s taking away the money we need to fund ourselves.”

The Amherst Industrial Development Agency, the other major such agency in Erie County, faces a $44,000 tab from the tax, which aims to raise as much as $5 million for the state government.

“It’s not really fair,” said James J. Allen, the Amherst agency’s executive director. “It’s a way of trying to get some money from IDAs.”

Agency officials said the new assessment could prompt changes in the way the development agencies do business. They could increase the fees they charge companies receiving incentives through the agency to recover the additional assessment, Allen said. Those fees now average around 1 percent of a project’s value.

Agencies also could stop serving as pass-through agencies that funnel federal or state grant money to companies. Those grants are counted as revenue for the IDA and are subject to the new 4.7 percent assessment on the agency’s annual revenues. The current assessments are based on 2008 revenues.

For the Erie County agency, about $2 million in passthrough grant funding in 2008 accounted for almost half of the agency’s bill under the new assessment.

“It’s certainly going to make me think very, very hard about spending $100,000 to do a favor for someone,” Culliton said.

Another option would be to charge the companies receiving the grants a fee equal to the assessment, Culliton said.

Mark J. Gabriele, counsel to the Niagara County agency, said the fee was part of last year’s state budget and drew little or no notice at the time. Gabriele, an attorney in the Harris Beach law firm, which represents several development agencies around the state, said the firm is researching a potential legal challenge.

“It’s a typical money grab by the state,” said Daniel E. Seaman, Town of Lockport attorney. “All the IDAs . . . are going to contact their legislators.”

Payments are due by March 31, the letter said.

David R. Kinyon, executive director of the Lockport agency, said the New York State Economic Development Council, a group of development agencies, wants to talk to the state about the methodology for determining the tab.

“IDAs are not public authorities under any definition of the term, but they were included,” Seaman complained.

Since the Niagara County agency was used as a passthrough agency for some major state grants, including those for construction of the new terminal at Niagara Falls International Airport, it had a high gross in 2008, even though it actually lost $113,000 on operations that year.

Robert A. Lipp, Town of Lockport budget director and IDA treasurer, said the town agency also lost money in 2008. But last year, it raked in fees from the Yahoo! data center project, for which it granted a tax break.

“When they come to look at 2009, when we made a million dollars, maybe [the fee] will be more than $900,” Lipp said.

“The lesson to be learned is, nothing is sacred,” Sloma said. “Everybody should guard their cookie jar, because you never know when the state is going to show up.”