In recent weeks, thousands of New York families have been told they no longer qualify for the popular School Tax Relief program. Many of them are about to learn they were the victims of a programming error by state tax officials.

“There were a lot of challenges in the data match,” said Jamie Woodward, executive deputy commissioner for the state Department of Taxation and Finance. In a hearing Monday on tax policy, she described how the administration of a new law to means-test STAR recipients went awry.

Because of a law legislators quietly passed last year, families with adjusted growth incomes of more than $500,000 no longer qualify for the STAR break, which can be worth hundreds of dollars per year.

To administer the new law — which is essentially a tax hike for high earners — Taxation and Finance sent files to the hundreds of local tax assessors around the state, listing families whose 2009 tax returns listed incomes over the limit.

But when local assessors sent out the notices to homeowners, they were flooded with calls from families who said they didn’t earn anywhere near $500,000 — and they brought in their tax returns to prove it.

“They’re supposed to be providing us with an updated list,” said Patricia McVee, the Bethlehem assessor. She sent out the notices to 255 families and has had 50 come back so far showing they are under the income limit.

Of the 255 — along with another 88 who fell into an “undetermined” income category — only two homeowners to date have been over the $500,000 limit.

McVee figures that ultimately, perhaps 20 Bethlehem families will actually lose their STAR exemptions. There are about 10,000 taxable residences in Bethlehem.

Clifton Park Assessor Walter Smead had the same experience. He sent out 131 notices to households that supposedly earned more than $500,000 and already has heard back from about 20 who have proved otherwise.

Woodward told lawmakers that the error stemmed from a programming error as well as difficulties in matching home ownership and income records. She stressed that the homeowners who were mistakenly identified as earning more than the $500,000 cutoff will still receive their exemptions.

Smead explained that there are a variety of ways such records can get confused. People may own a home in a trust, or the names on an ownership deed may differ from a married name.

“There are ways to set up (home) ownership that may not mirror how they file their income tax,” he said.

Another potential snag: If someone rolls over or switches a 401(k) retirement plan, that could show up as a $500,000-plus income even though it doesn’t represent earnings, said John Franck, Saratoga Springs’ commissioner of accounts. “There are a lot of very irate people,” said Franck, who also serves as assessor, of the reaction to the denial letters his office had to send out. “Today alone I probably received 15 nasty calls on this.”

Taxation and Finance spokesman Jeffrey Gloak said they didn’t yet know precisely how many New Yorkers, from an original estimate of about 64,000, would ultimately lose or keep their STAR tax break. “We’ve asked them to hold off sending denial letters,” Gloak said of assessors who hadn’t sent the notices.

Woodward’s remarks came during Monday’s joint Assembly-Senate budget hearings on taxes. The hearings came amid a push by public employee union-backed groups to persuade lawmakers that an income tax surcharge for those earning more than $200,000 should be extended past its sunset date at the end of 2011.

“We’re really looking at two New Yorks,” said Ron Deutsch, of New Yorkers for Fiscal Fairness, one of several organizations that want the surcharge to remain in place. Speaking a forum nextdoor to the tax hearings, Deutsch noted that the wealthiest 1 percent of New Yorkers pay 8 percent of their income toward state and local taxes while the bottom 80 percent pay 11 percent.

On the other side, economists have noted that the wealthy provide a large percentage of the total of tax receipts received by government, and too many taxes could drive those people out of the state.

In the tax hearing, E.J. McMahon of the Empire Center for Public Policy noted that inheritance taxes in the Empire State are higher than federal levels, and numerous people leave New York for states where those taxes are lower.

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