Foreign Minister Marise Payne has discussed alleged war crimes committed by Australian troops with Afghanistan's President Ashraf Ghani during a lightning-quick visit to Kabul.

Senator Payne flew into Afghanistan on Sunday afternoon after holding a series of meetings and summits in Europe.

The stopover was not flagged for security reasons. A bomb went off in Kabul only the day before Senator Payne arrived, killing at least 68 people, most of them schoolchildren.

Senator Payne met Mr Ghani and the chair of Afghanistan's High Council for National Reconciliation, Abdullah Abdullah.

She also held meetings with the commander of United States troops in Afghanistan, General Austin Miller to discuss the withdrawal of troops from the country.

Senator Payne left Afghanistan on Sunday evening, after several hours in the country. 

The federal government announced last month that the 80 or so remaining Australian soldiers in Afghanistan would pull out of the country by September, in line with the US military withdrawal.

Australia is also grappling with the legacy of the almost two-decade-long war in Afghanistan.

The relationship between the two countries has been rocked by the findings of the Brereton Report, which found there was "credible evidence" that Australian soldiers unlawfully killed at least 39 civilians during the conflict.

The Defence Department has already begun the process of expelling more than a dozen soldiers in the wake of the report, and recently appointed Rear Admiral Brett Wolski to head a taskforce that will shape what it does next.

A special investigator is also probing potential criminal prosecutions.

The Foreign Minister only briefly mentioned war crimes in the statement, saying she "discussed the recent Inspector-General report, Australia's robust response, and the establishment of the Office of the Special Investigator" with leaders in Afghanistan.

Her visit comes at an uncertain and fraught moment for Afghanistan.

In September last year, Afghanistan's government began peace talks with the Taliban in Qatar, but the discussions faltered earlier this year when the Taliban protested the US timeline for withdrawal. In recent weeks, there has been yet another surge in violence in the country.

The car bomb that went off the day before Senator Payne arrived was outside a girls' school.

Most of those killed were young girls who attended the school, which largely served the Shiite Hazara community.

The Foreign Minister condemned the atrocity on social media, saying she expressed her "deepest condolences" to Mr Ghani on the "cowardly terrorist attack".

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In the statement, Senator Payne said Australia wanted to see "a sustainable peace that is genuinely inclusive and involves all of Afghan society".

"During [my] meetings, we discussed the sacrifices made by the Afghan people, as well as those international military forces killed or wounded, including those Australians who made the ultimate sacrifice and the many who still bear the impacts of their service in Afghanistan both physical and mental," she said.

She said the Australia-Afghanistan relationship would enter a "new chapter" in the wake of the military withdrawal.

Senator Payne also emphasised that Australia would press ahead with its aid and development assistance program in Afghanistan.

She met with Afghanistan's Women's Affairs Minister Hasina Safi "to discuss how Australia and Afghanistan have worked together to support and improve the rights of women and girls — a development we want to see maintained", the statement said.