Warren Group, a Boston company that tracks local real estate, reported that home sales in September dropped by 12.9 percent compared with the same month last year, the worst September showing in three decades.

Only 3,285 single-family homes sold in September, down from 3,771 during the same month last year, according to Warren Group.

Sales in the third quarter fell more than 20 percent compared with the same period in 2009 — making it the slowest third quarter since 1990.

The anemic sales were largely expected because they stack up against last year’s figures, when home buyers were scrambling to qualify for the federal tax credit. The credit offered qualified buyers as much as $8,000 if they signed a contract on a property by April 30 and closed by Sept. 30. With the contract deadline as an incentive, buyers snapped up homes through the first part of the year.

Real estate agent Christy May said that sales of moderate- to high-priced homes are now starting to rebound, but first-time buyers remain largely absent from the market.

Those buyers “were all tapped out’’ during the period when the tax credit was available, said May, who works for RE/MAX Landmark in Westwood.

Angela Harkins, a real estate agent in Westford, said potential buyers are showing up at open houses this fall, but many are still hesitant to make a decision. “It has been a slower than typical fall,’’ she said. “It’s not dead.’’

While median prices for single-family homes rose slightly in September to $287,000 — a less than 1 percent rise compared to the same month in 2009 — this is the slowest increase in home values in 10 months, said Timothy M. Warren Jr., chief executive of Warren Group. If the slowdown continues, values could head down back down next month, Warren said. “We could see a reversal of this trend,’’ he said.

Condominium sales also fared poorly last month, off 21. 5 percent compared with the same month in 2009. At the same time, prices crept up to $262,425 — about a 1 percent increase from September last year, Warren Group said.

In other downbeat housing news, the S&P/Case-Shiller Home Prices Indices reported yesterday that Boston area home values fell 0.3 percent in August compared with July. It was one of 17 metropolitan areas out of 20 that showed falling home values in August based on repeat sales.

“Home prices broadly declined in August,’’ said David M. Blitzer, chairman of the Index Committee at Standard & Poor’s. “It does not seem that any of the markets are hanging on to the temporary momentum caused by the home buyer’s tax credits.’’

Buyers are staying away from the market despite significant drops in housing prices since their peak in 2005 and historically low mortgage rates, which are hovering above 4 percent for a 30-year fixed rate loan.

Karl E. Case, cofounder of the Case-Shiller index and a senior fellow at the Joint Center for Housing Studies at Harvard University, said he believed borrowers will eventually head back into the market.

He said that despite uncertainty, people who plan to be in one location for at least five years should still consider purchasing a home. “If you can afford the payments and you like the bloody thing, it is a terrific time to buy,’’ Case said.

Jenifer B. McKim can be reached at jmckim@globe.com.