The Japanese government announced the temporary halt last month for "concentrated discussions" with Takeshi Onaga, the outspoken governor of Okinawa, and other officials.
But negotiations failed to reach a compromise and work has now resumed.
The plan to relocate Futenma air base, first mooted in 1996, has become the focus of anger among locals, who insist it should be shut and a replacement built elsewhere in Japan or overseas.
Henoko is a small coastal area on Okinawa.
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Reports added Onaga also immediately condemned the resumption, saying "It was extremely regrettable. I will not let (the central government) build a new base in Henoko by any means."
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.
The legislation, which Abe says is necessary to counter rising regional tensions, has sparked rare protests in Japan.