But there was less of a fall compared to each of the previous three months, with the annual rate of decline easing to 3.3%, compared with 4.8% in August.
The figures are the first to be released after the Government's £1 billion package to help homeowners and buyers was announced. This included abolishing stamp duty on properties costing up to £175,000 for a year.
The statistics show there was an increase in the number of properties coming on to the market costing between the old threshold of £125,000 and the new one of £175,000 of only 0.5% .
However, a 5% fall in the number of homes priced between £175,000 and £200,000 was reported.
Miles Shipside, commercial director of Rightmove, said: "The housing market is on its knees and will remain so until financial institutions address the disastrous state of the mortgage funding markets."
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