The Trans-Pacific Partnership (TPP), a vast agreement that would cover about 40 per cent of the global economy, is a key plank in Obama's bid for a renewed focus on Asia.
It is also seen as crucial for Japanese Prime Minister Shinzo Abe's pledge to shake up his country's long-lumbering economy.
But the ambitious 12-nation deal has stalled as Tokyo and Washington lock horns over key details, including Japanese tariffs on agricultural imports and US access to its ally's major auto market.
"Now is the time for bold steps," Obama told reporters.
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"I think it's fair to say that there are certain sectors of the Japanese economy -- the agriculture sector, the auto sector -- in which market access has been restricted historically."
He added that those stumbling blocks "at some point have to be resolved...(and) I believe that point is now".
The deal is a crucial part of Abe's promises to reform Japan's economy and stoke long-tepid growth, the US leader said.
The two leaders told their trade delegations to press on with talks to "settle the remaining issues and work for an early conclusion" of the agreement, Abe said.
Japanese economy minister Akira Amari said negotiations were still moving forward, after holding the latest round of meetings with US Trade Representative Michael Froman in Tokyo today.