A remote Afghan province in which Australia spent hundreds of millions of dollars, and lost numerous lives trying to secure, is having serious governance and security problems less than two months after the Australians left.

Hundreds of angry rural residents flooded into the Oruzgan capital, Tarin Kowt, last week, burning tyres, blocking roads and closing down business in a five-day protest about alleged corruption and collusion with the Taliban by the provincial government.

The violence, linked to a rift between Governor Amir Mohammad Akhundzada and police chief Matiullah Khan, raises questions about the long-term stability and security of the south-central province that Prime Minister Tony Abbott in December described as being a ''better place'' for Australian troops' involvement.

A local official, who asked not to be named for personal safety reasons, briefed Fairfax Media on the situation, saying protesters had alleged corruption involving the governor, overseas aid projects and Taliban collusion. They were also furious about the governor's alleged corruption links to road works connected to aid projects.

However, last week's protest was cut short after the central government ordered Mr Akhundzada and the police chief to Kabul. But protesters remained in Tarin Kowt ready to continue if their concerns were not addressed, he said.

The official's claims were confirmed by a former employee of the Australian military and contractors in Oruzgan.

Mr Akhundzada vigorously denied the allegations on Friday, saying they were "a lie" being promoted by Mr Khan.

"I am sure the people and all tribes in Oruzgan are with me for the rule of law and reforms,'' Mr Akhundzada said. ''This is absolutely a problem between me and Matiullah Khan, the police chief.''

Efforts to contact Mr Khan this week were unsuccessful.

Australia's Foreign Affairs Department confirmed it was aware of the "current events in Oruzgan" but linked them to the presidential and Provincial Council elections scheduled for April 5.

The DFAT spokesman said he was unaware of any allegations involving the governor and the aid projects.

''It is not clear that the allegations relate to activities funded by DFAT [or the former AusAID],'' the spokesman said. "However, if credible allegations of corruption in DFAT AusAID funded projects were passed to us we would investigate in accordance with DFAT's fraud control policies.''

Earlier Mr Abbott marked the troops' departure by thanking them for their work and saying their sacrifices had "not been in vain".

The United Nations said the number of civilians killed and wounded in Afghanistan rose 14 per cent last year, as NATO troops drew down after more than a decade of war.

A total of 8615 civilian casualties were recorded in 2013, with 2959 killed and 5656 wounded, according to the UN Assistance Mission in Afghanistan's annual report.

More than 50,000 NATO-led combat troops who are still in Afghanistan are due to leave by the end of this year.