AFL executives Simon Lethlean and Richard Simkiss have been forced to resign following accusations of misconduct.

The pair stood down in the wake of allegations two senior AFL managers had affairs with younger female employees.

Earlier in the week the Herald Sun reported AFL insiders were concerned with how women were being treated at the organisation, prompting whistleblowers to bring the controversial relationships into the public sphere.

Lethlean was General Manager of Football Operations and Simkiss was General Manager of Commercial.

AFL CEO Gillon McLachlan addressed the media on Friday afternoon and said he was "disappointed" in what had transpired but thinks their decision to resign is "the right one".

"Two men had inappropriate relationships with two younger women who work in the AFL industry," McLachlan said.

"The AFL that I want to lead is a professional organisation based on integrity.

"I expect my managers to be role models and set a standard for the rest of the organisation. They are held to a higher standard.

"I want a diverse and inclusive culture where employees are treated respectfully and fairly at all levels.

"It must be backed up with action and change."

McLachlan said numerous parties are involved in this situation and asked the media to respect their privacy.

He said the resignations were based on separate matters of a "professional and personal" nature, but he was only dealing with the professional component.

Lethlean was newly promoted and had only been in his role for a few months.