A Defence Ministry statement said the blast, less than 110 kilotons, was detonated underground at 23.30 GMT.
The September explosion, at Mururoa atoll, was less than 20 kilotons, roughly equivalent to the bomb dropped on Hiroshima in 1945. Last night's explosion was the second in a series of six to eight tests. The experiments are due to end by next May.
The Fangataufa explosion came several hours after French commandos seized the Greenpeace protest ship Manutea, the group's fourth and last vessel stationed near the test sites.
The ship was seized in international waters, leading Greenpeace to call the seizure illegal and to state that the next test was imminent.