The decision came days before the new rules come into force, an event expected to prompt multiple requests from power companies for the green light to get their atomic plants operating.
It pushes back the likelihood of Japan being without any working reactors in the immediate future.
The Nuclear Regulatory Authority concluded that Units 3 and 4 at the Oi nuclear plant in western Japan are "not in the condition that would pose immediate safety concerns" even without being inspected under the new safety rules.
"I expect the operator will continue improving the safety of the plant towards meeting the new standards," said the nuclear authority's head Shunichi Tanaka.
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The body will also continue examining if there are any active tectonic faults underneath the plant.
The stricter new standards are part of a government effort to convince a sceptical populace that they are taking safety issues seriously in post-Fukushima Japan.
Leading figures in a vocal anti-atomic movement say the nuclear industry had too cozy a relationship with its regulators in the decades leading up to the tsunami-sparked disaster in March 2011.
Fukushima operator TEPCO said yesterday it would ask the NRA for permission to restart reactors at the world's largest atomic power station at Kashiwazaki-Kariwa in Niigata prefecture, north of Tokyo.
Japan's power companies have been badly hit by the surging cost of producing electricity from fossil fuel alternatives since their reactors were shut down.
Resource-poor Japan has to import the coal, gas and oil it is using to replace nuclear generating capacity and the falling value of the yen has pushed up the relative cost of those dollar-priced commodities.