It was the first time that prices have risen since the government started releasing the data in April to add transparency to the market after the shutdown of all nuclear plants following the Fukushima crisis sent fuel prices spiralling.
Spot LNG contracted in September for delivery to Japan averaged $13.20 per million British thermal unit (mmBtu), a rise of $1.80 from a month earlier, the Ministry of Economy, Trade and Industry (METI) said.
Asia spot LNG prices have risen nearly 40 percent from a three-year low in July to $14.60 per mmBtu last week as buyers in the region stock up their tanks to get ready for the cold season.
Japan, which takes about a third of the world's LNG imports, shipped in a record 87.73 million tonnes in the year through March.
The average spot price is based on about 10 percent of the nation's purchases of the super-chilled fuel.
The average LNG price released by METI was also intended to be a reference for a futures contract for the fuel, which the Tokyo Commodities Exchange (TOCOM) plans to launch next year, as part of attempts by Japan to cut costs.
TOCOM and Singapore-based broker Ginga Petroleum began offering non-deliverable LNG forward contracts last month as an initial step, but so far there have been no trades of the derivatives, a market official said on Thursday.
The METI survey looks at samples of fixed prices for LNG sold to power companies and utilities among others, and excludes spot deals linked to benchmark prices such as the US natural gas Henry Hub index.