North Korea is expected to press for a settlement over Japan's occupation of the Korean peninsula from 1910-1945.
Despite their long-standing differences, both sides have expressed cautious optimism over the talks – perhaps boosted by signs that the deadlock over the North's nuclear programme is finally thawing.
"If they want to first talk about the settlement of the unfortunate past, we are prepared to do that," Japan's chief envoy, Yoshiki Mine, told reporters before the meeting began.
His North Korea counterpart, Song Il Ho, said he was hoping for "serious achievements" from the talks.
Nobutaka Machimura, Japan's foreign minister, also sounded hopeful as the new round of talks got under way.
"Obviously, the abduction issue will be taken up. We will also talk about how well we can settle the unfortunate situation between Japan and North Korea," he told reporters in Sydney, where he is attending the summit of the Asia-Pacific Economic Co-operation (Apec) forum.
He said: "I think there appears to be a sort of progressive momentum in the six-party talks.
"In this environment, I hope that the Japan-North Korea talks will go as well as they can."
The last round of the same Japan-North Korea working group took place six months ago in Hanoi, only to break down in acrimony after the North reportedly objected to Japan's position on the unresolved abductees.
North Korea has acknowledged kidnapping 13 Japanese in the 1970s and 1980s in a bizarre scheme to train its spies in the ways of the outside world.
It returned five abductees and their families in 2002, but says that the rest are dead and the issue is closed.
Japan has insisted those cases and other disappearances remain unresolved.
Until a satisfactory explanation is given, Tokyo has said there can be no improvement in relations.
As a result Shinzo Abe, the Japanese prime minister, has broken ranks with the United States by refusing to fund February's disarmament-for-aid deal with North Korean.
In recent months however, Abe's government has been severely weakened electorally and there are signs Japan's hard-line stance may be easing.
Some members of Abe's own party, for example, have voiced fears that his hardline stance has isolated Japan from its main ally, the United States.