The Home Affairs Department cancelled the visa of at least one Nigerian, in Australia on a student visa, on the basis the permit had been obtained as a result of the fraudulent conduct.

However, Ogochukwu Concilia Odinkaeze successfully challenged the cancellation in the Administrative Appeals Tribunal.

The Home Affairs Department confirmed two non-Australian citizens had their employment at the high commission terminated following "internal disciplinary investigations".

The department would not confirm the number of visas issued by the staff members, but said an investigation had assessed the "visas issued by these individuals ... and appropriate action taken where necessary".

Details of the scam were outlined in Ms Odinkaeze's bid to continue her nursing studies in Australia.

According to an AAT judgement, published last week, the scam worked by the staff bypassing a system which allocated cases, allowing them illegally to approve visas to Nigerian applicants, who had been identified as high risk, based on their nationality.

The racket was discovered by the Home Affairs Department, which then identified a link between offshore nationals engaging in criminal activity and visas granted by a department officer working at the Australian high commission in Pretoria.

As a result, Home Affairs launched a joint investigation with the Australian Commission for Law Enforcement Integrity in early 2017.

The investigation found that locally engaged staff in the office of the Australian high commission in Pretoria had been paid to approve visas to Nigerians.

Australian missions often employ locally engaged staff to undertake research, administrative and support roles.

Locally engaged staff do not have diplomatic or consular status, privileges or immunity, and wages and conditions are based on local labour laws and labour market conditions.

The corrupt system meant staff did not follow the rigorous assessment process that would have been applied to Nigerian applicants as part of department’s risk profiling.

It is alleged that the staff has been paid by third parties who were associated with Nigerian students.

There is no allegation Ms Odinkaeze paid to have her visa approved.

The tribunal heard her application for a student visa had been processed by one of the allegedly corrupt officers in February 2017.

The application was allocated to the officer in a way that bypassed established case management processes.

The tribunal heard Home Affairs, as a result, had a reasonable suspicion Ms Odinkaeze's visa was obtained as a result of fraudulent conduct.

However, in a joint decision, tribunal deputy president Jan Redfern and member Dr Colin Huntly overturned the decision to rescind her visa as they had not been satisfied by the grounds for cancellation.

"There is no evidence that Ms Odinkaeze knew of the fraud and, without evidence to the contrary, we accept her evidence that she did not know and was not involved in any fraud," the member wrote in their decision.

"While the circumstances surrounding the granting of Ms Odinkaeze's student visa are suspicious, there must be some evidence on which to base a suspicion of the necessary causal link.

"Mere surmise or conjecture simply because of the other cases is not sufficient to establish a reasonable suspicion.

"There could be many explanations for why Ms Odinkaeze's visa was processed by the allegedly corrupt department officer outside the usual case management process."

Home Affairs said it took all allegations of misconduct and corruption seriously.

"Robust action is taken against individuals where corrupt conduct is identified," a spokeswoman said.

It's not the first time the high commission in Pretoria has come under investigation for corruption.

In about 2010, DFAT's conduct and ethics unit and passport fraud section travelled to London to find a former South African employee accused of stealing Australian passports.