A former Government minister is being investigated by police for allegedly using his ex-MP perk of taxpayer-funded flights on business trips and then claiming driving mileage from the charity he headed.

Detectives have executed search warrants on the Auckland home of Roger McClay, a National Party MP for 15 years, and seized financial records from Keep New Zealand Beautiful, of which he was the chairman.

Former staff and fellow board members have also been interviewed by police.

Mr McClay, 64, is under investigation for allegedly invoicing the environmental organisation for the cost of driving mileage, but taking a taxpayer-funded flight instead.

As a former MP, Mr McClay is entitled to the 90 per cent subsidy for 12 domestic return flights each year. No charges have been laid and he has denied any wrongdoing.

He said he was disappointed at the length of the police inquiry but declined to comment further.

Mr McClay resigned as Keep NZ Beautiful chairman in July to take up a position at the NZ Spinal Trust.

During his time in Parliament, until 1996, he held positions as Minister of Youth Affairs and Associate Minister of Education and Social Welfare.

He was then appointed the Commissioner for Children and in 2005 was made a companion of the Queen's Service Order in recognition of his public service and contribution to the welfare of children.

More recently, Mr McClay - whose son Todd is National MP for Rotorua - has worked for a number of charities, including Keep New Zealand Beautiful.

A source said the Parliamentary Service, which administers MPs' travel subsidies, spoke to Keep NZ Beautiful chief executive Simon Johnston last December.

Mr Johnston, who had been in the job for only three months, was then interviewed by detectives from the Glen Innes CIB in February.

He has recently resigned to take up another job and referred all queries to Tony Rush, who has replaced Mr McClay as chairman. His resignation was not connected with the police investigation.

A search warrant was executed on Mr McClay's home in June and detectives also spoke to Iris Donoghue and Ben Lightfoot, the vice-chairs of Keep NZ Beautiful.

They also interviewed former chief executive Barry Lucinsky in October. He was in the job for most of Mr McClay's time on the board and said he had the "utmost respect" for him.

"At no time, did I have any doubt or any suspicion or any proof that Roger McClay has done anything wrong. I think he's an honourable man.

"I've spent a lot of time with him. He's a bloody good guy and I think it's bloody ridiculous. I used to verify all his accounts and I never had reason to question him."

Asked if Mr McClay was invoicing the charity for full travel costs but allegedly claiming the MP subsidy, Mr Lucinsky said: "I don't know. And I'm being honest. How would I know that?"

Mr Rush, the new chairman, said Keep NZ Beautiful had provided all the paperwork the police had requested.

He said the police inquiry played no part in Mr McClay's decision to resign.

"Roger had indicated very early on in his last term that it was time for a change. To some extent it was a matter of timing," said Mr Rush.

"I feel for Roger personally. He threw himself heart and soul into the job of being chair of Keep NZ Beautiful. He believed in the organisation. He had its best interests at heart."

The police inquiry was headed by Detective Senior Sergeant Greg Cramer, who has since moved to the North Shore as a detective inspector.

Spokeswoman Noreen Hegarty said police do not "disclose the identities of people under investigation".

A spokesman for the Parliamentary Service refused to answer questions about Mr McClay's travel claims.