The latest figures were lower than an initial estimate of 0.5 per cent growth in the July-September period, with exports also under pressure.
The weak reading translates into annualised growth of 1.3 per cent, far below the median market forecast of an annualised 2.3 per cent expansion.
But the government did offer a glimmer of hope, slightly revising up growth figures for the first and second quarter, as spending ticked up.
And while Japan's recovery has been unsteady, the economy is "growing bit by bit", said Takeshi Minami, chief economist at Norinchukin Research Institute in Tokyo.
"But it will carry on growing steadily even though the number may not be that strong."
Japan's economy contracted in the last three months of 2015, before bouncing back this year although the recovery has been wobbly.
That is putting Japanese officials under increasing pressure to deliver as more and more economists write off Prime Minister Shinzo Abe's bid to cement a lasting recovery, dubbed Abenomics.
Separate figures last month showed that Japan's factory output ticked up in October, expanding for the third month in a row, but spending among Japanese households was still struggling.
Next week, Japan's central bank will release its closely-watched Tankan business sentiment survey.
Abe came to office in late 2012 and launched a growth plan - a mix of massive monetary easing, government spending and red-tape slashing.
The plan sharply weakened the yen - fattening corporate profits - and set off a stock market rally that spurred hopes for a once-soaring economy caught in a deflationary spiral of falling prices and lacklustre growth.
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