The one-month delay comes as Prime Minister Shinzo Abe is seeing his popularity plunge, largely owing to his efforts to expand the role of pacifist Japan's military.
Yesterday, top government spokesman Yoshihide Suga said construction would be suspended from August 10 until September 9.
The plan to relocate Futenma air base, first mooted in 1996, has become the focus of anger among locals, who insist it should be shuttered and a replacement built elsewhere in Japan or overseas.
Takeshi Onaga, the combative governor of Okinawa, told local media that the temporary construction halt was a "positive step".
Both Tokyo and Washington have repeatedly backed the relocation plan, with Abe insisting it was "the only solution".
All sides agree that Futenma's current site -- in the middle of a crowded urban area where its aircraft are a nuisance to thousands of locals -- is not appropriate, but the US will not close it until a replacement facility is ready.
Henoko is a small coastal area on Okinawa.
Asked why it had been delayed, Toner said: "These are discussions that need to take place between local authorities and the government of Japan."
Abe has faced opposition over the Okinawa plan and his public opinion ratings are dropping as parliament debates controversial legislation aimed at changing the Japanese military's narrowly defencive role.
The legislation, which Abe says is necessary to counter rising regional tensions, has sparked rare protests in Japan.
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