Australia's incoming foreign minister Julie Bishop said Sunday that the new conservative government would work with Indonesia "where we need to" but it was not seeking permission to implement controversial refugee policies.

Bishop, prime minister-elect Tony Abbott's nominee for top diplomat, said Australia respected Indonesia's sovereignty but it would forge ahead with sensitive plans to combat people-smuggling that were met with a cool response in the Southeast Asian nation during the election campaign.

Abbott plans to tow back asylum-seeker boats from Indonesia in a military response codenamed Operation Sovereign Borders, while buying up fishing boats to keep them from the hands of people-smugglers, embedding Australian police in villages and paying locals for intelligence.

Indonesia's Foreign Minister Marty Natalegawa said Jakarta would reject the plans as not in the spirit of partnership between the two countries last week, adding that the issue would be a top priority for talks with Abbott ahead of next month's APEC summit.

But Bishop insisted that the policies would be implemented in a television interview on Sunday.

"Over the next few days and weeks we will be working cooperatively with Indonesia. But I point out we're not seeking Indonesia's permission to implement our policies, we're seeking their understanding," Bishop told Meet the Press.

"We will work cooperatively with Indonesia, where we need to," she added.

Bishop said Australia respected Indonesian sovereignty and defended on-the-ground intelligence operations and payment of bounties.

"The IOM (International Organisation for Migration) is already operating in Indonesia collecting intelligence. And the idea of financial rewards, for example, for information, is hardly novel. The United States has been doing it for decades," she said.

"We have policies that we wish to implement as soon as we're sworn in, and we will be working with Indonesia through a series of bilateral meetings and broader meetings that will occur as soon as I'm sworn in," added Bishop.

Abbott's Liberal-National coalition ended six years of centre-left Labor rule with an emphatic election win last weekend. A "Stop the Boats" plan was a central plank of his campaign strategy.

Asylum-seekers arriving in Australia on unseaworthy, overcrowded vessels from Indonesia are a sensitive political issue, despite their relatively small numbers by global standards, with both Abbott and Labor incumbent Kevin Rudd making hardline promises in a bid to win votes.

Along with his Indonesian activities Abbott plans to put all asylum-seekers arriving by boat -- including those already in Australia awaiting processing -- onto temporary three-year visas and strip them of appeal, family reunion or permanent residency rights as well as access to legal assistance. They will be forced onto work-for-welfare programmes.