A high-ranking police officer has resigned after his superiors were alerted to an affair he had with a junior colleague.

Superintendent Jon Moss was in charge of the department that recently ordered police officers to disclose office romances, but resigned from his Wellington-based role after failing to report his relationship with a constable.

He had been on annual leave since police hierarchy became aware this month of an undisclosed historical relationship with the officer.

A week ago, police national headquarters spokesman Jon Neilson said police were "looking into a number of issues raised about a relationship that ceased a number of years ago".

Yesterday, Mr Neilson confirmed Mr Moss had resigned but could not comment further.

The Weekend Herald understands the woman involved is no longer a police officer and laid a complaint about the alleged "double standards" of Mr Moss a few weeks ago.

Mr Moss helped introduce the new "professional distance policy" last year which covers sexual conduct for officers with the public, victims of crime and work colleagues.

Although the affair occurred before the new rules were introduced, Mr Moss is believed to have resigned because the affair could be perceived as hypocritical of his role as the national head of police professional standards.

The rules were written after the Commission of Inquiry into police conduct, in which Dame Margaret Bazley recommended a code of conduct be introduced for officers.

According to the new policy, relationships between officers where there is a "power imbalance" - such as supervisor and employee - are considered unethical.

The relationship must be declared if the senior officer cannot "take steps to manage the risks to the organisation".

An anonymous letter to the Police Association published in August last year described the boundary rules as a "good laugh".

"By cripes, I don't know what spinster wrote this but obviously no one who has had any experience with anatomy or watched a good old-fashioned soap opera.

"I also wonder whether this paperweight will be retrospective and some of our 'high flyers' with pips, at certain police institutions, will have to revisit 'now disclosed' relationships and continue that road up the ranks alone.

"In reality, I find this all very sad. What happened to good old common sense in the birds and the bees arena?"

Mr Moss moved to Wellington from the Auckland CIB about 18 months ago and was promoted to superintendent as the head of professional standards.