Australia's aid agency says it has recently become aware that one of its international partners faced fraud allegations in Afghanistan last year.

Documents provided by AusAID reveal that International Relief and Development (IRD) was being investigated over allegations of kickbacks and bribery by senior employees.

IRD was also accused of significant waste and mismanagement in a $500 million Afghan roads program.

AusAID says it has made inquiries to find out why it was not informed earlier.

"We sought urgent advice from IRD on the substance of these allegations and why AusAID was not informed," the agency said in a statement.

"IRD's response, and other AusAID inquiries with the US government, indicate that there is no active fraud investigation underway involving IRD.

"AusAID has zero tolerance for fraud."

AusAID says the allegations relate to programs implemented under an agreement with the US, and do not relate to Australian programs.