"Other data suggest a market beginning to shift to slower growth rather than one about to accelerate," said David Blitzer, chairman of the S&P Dow Jones index committee.
The Case-Shiller index covers roughly half of U.S. homes. It measures prices compared with those in January 2000 and creates a three-month moving average. The September figures are the latest available.
Monthly price gains slowed in 19 of the 20 cities tracked by Case-Shiller index. Prices rose 1.3 percent in Las Vegas compared with a 2.9 percent month-to-month gain in August. Home prices rose just 0.2 percent in Tampa, Fla., after a 1.8 percent gain in August.
Charlotte, N.C., was the only city where prices declined from August to September.
Year-over-year, prices jumped 13.3 percent from September 2012, the fastest such gain since February 2006. Those gains may be putting some homes out of reach for many buyers. Mortgage rates have also risen since the spring, though they remain low by historical standards.
And the government shutdown delayed some sales in October because the IRS was unable to verify incomes, a critical part of the mortgage-approval process.
Home resales fell in October for a second straight month to a seasonally adjusted annual pace of 5.12 million, the lowest since June. That pace is still 6 percent higher than it was a year earlier. But it's below the roughly 5.5 million annual sales pace typical of a healthy market.
In addition, a measure of signed contracts to buy homes fell for a fifth straight month in October. That suggests that final sales will remain weak in coming months.
In October, signed contracts plunged in the West, where price gains have been the strongest. The Case-Shiller index showed that prices jumped more than 29 percent in Las Vegas compared with a year ago and nearly 26 percent in San Francisco.
Many economists argue that the Case-Shiller figures overstate recent price gains because the figures include foreclosed homes. Foreclosed homes usually sell for low prices, and as the proportion of foreclosed sales declines, that can push up price gains.
In other housing news, U.S. homebuilders planned to build apartments in October at the fastest pace in five years, a sign they expect a jump in rentals in coming months.
The Commerce Department says plans to build houses and apartments were approved at a seasonally adjusted annual rate of 1.034 million. That's 6.2 percent higher than the September rate of 974,000 and the fastest since June 2008, just before the peak of the financial crisis.
Nearly all of the increase was for multi-family homes, a part of residential construction that can be volatile. Those permits rose 15.3 percent to a rate of 414,000.
Permits for single-family houses rose 0.8 percent to a rate of 620,000.
The government report did not include information on homes started. That was delayed again by last month's government shutdown.
Associated Press reporter Josh Boak contributed to this report.