Home sales declined from 5.39 million per year in August to a seasonally adjusted annual rate of 5.29 million in September, the trade group said.
The figure on existing home sales for August was revised lower from 5.48 million.
Sales for the month are also 10.7 percent higher than September 2012 when the annual rate stood at 4.78 million.
NAR also said the median price of a home in September rose 11.7 percent from the same month in 2012, marking the 10th consecutive month of increases of 10 percent or more.
The trade group said tight inventory of available homes is putting pressure on prices, which threatens the housing market recovery.
"Affordability has fallen to a five-year low as home price increases easily outpaced income growth," said NAR Chief Economist Lawrence Yun.
"Expected rising mortgage interest rates will further lower affordability in upcoming months. Next month we may see some delays associated with the government shutdown," Yun said in a statement.
The trade group said there were 2.21 million existing homes on the market at the end of September, which represents a 5-month supply at the current sales pace, a figure that is up from the 4.9-month supply in August, NAR said.
Unsold inventory is 1.8 percent higher than September 2012.