The Federal Government is investigating the financial affairs of a major GP training provider, amid questions over hundreds of thousands of taxpayer dollars it has been spending on marketing and web development.

General Practice Training Queensland (GPTQ) is responsible for more than 500 GP registrars.

But earlier this year, its CEO, Peter Harrison, and its chief operational officer suddenly left the organisation after the pair were accused of financial mismanagement by senior GPTQ employees.

A forensic audit found the organisation had spent up to $3 million on contractors over a three-year period, with minimal documentation or evidence of work performed.