A key witness who testified before the state capture inquiry has fled the country, saying she fears for her life.

Koroneka Trading and Projects director Babadi Tlatsana told the commission in June that her company was "hijacked" by an SA Express manager and used as a conduit to siphon money from the airline and the North West government into the bank accounts of certain individuals.

The commission's evidence leader, Kate Hofmeyr, on Thursday announced that the commission had received an affidavit from Tlatsana's lawyer saying she had left the country. According to the affidavit, relayed by Hofmeyr, Tlatsana believed "strange" men were following her and monitoring her premises in Mafikeng.

Tlatsana then left the country to an unknown destination.

Deputy chief justice Raymond Zondo said it was "concerning" and asked his team to keep him updated on the matter.

The commission previously heard how the North West's department of community safety and transport management had underhandedly struck a deal with SA Express to have the airline operate local routes to and from each airport.

The deal, which is riddled with allegations of corruption and procurement irregularities, was allegedly envisaged to move up to R400m out of the North West provincial government accounts and into SA Express.

The commission believes R97m of that total amount was siphoned off to various entities through a "detailed scheme of money laundering" which involved Koroneka.