Foreign ministers Julie Bishop and Retno Marsudi have restored their bond after Indonesia's execution of two Australian citizens set the relationship back for six months.

Three months after Myuran Sukumaran and Andrew Chan were sent to the firing squad for their decade-old drug smuggling offence, the ministers met face-to-face in Kuala Lumpur, Malaysia.

The pair greeted each other with a kiss, before talking for around 30 minutes, at one stage excluding staff from the room.

Ms Retno, describing Ms Bishop as a "good friend", said the talks had been productive.

They would meet again before the end of the year in "two plus two" talks, when both nations' foreign and defence ministers would discuss security issues, Ms Bishop said.

Trade Minister Andrew Robb would lead a large business delegation to Jakarta to investigate investment opportunities.

Ms Bishop predicted the relationship would go "from strength to strength" and gave her personal thanks to her counterpart for her friendship and "willingness to be available to me and answering my text messages at any time of the day or night".

The warm interaction follows a difficult six months for Australia and its neighbour.

In February, after Jakarta signalled its intention to execute Sukumaran and Chan, Ms Bishop gave an emotional speech to parliament.

She said the two men didn't deserve to pay for their crimes with their lives and that she had talked with the mothers of both men.

She had a "tense" phone call with Ms Retno followed by a letter that offered to pay for both men to be jailed for life, if a prisoner exchange could not be organised.

But the letter that began "My dear Retno" was rebuffed by an angry Jakarta, which resented its contents being revealed in the media.

Months of intense diplomatic efforts failed to move Indonesia, where President Joko Widodo argues the death penalty is a deterrent in a "drugs emergency".

After Chan and Sukumaran became the first Australians to be executed in Indonesia on April 29, Paul Grigson became the first ambassador to be recalled.

Ministerial contact was also suspended.

Mr Grigson returned to Jakarta in June to a new controversy, this time around claims Australian officials paid an asylum seeker boat to turn back to Indonesia.

That issue, as well as the shock reduction in Indonesia's live cattle order this quarter, were to be discussed behind closed doors.

Ahead of the meeting, Ms Bishop was adamant the relationship remained strong.

"We do face challenges from time to time," she told reporters.

"It's how we respond to them, how we recover from them, that I think is important."