The man, a structural engineer from Remuera, will appear in Auckland District Court this afternoon.
There have been no confirmed sightings of Ms Thomas, also 32 from Remuera, since June 27.
Her bank accounts had not been touched, and she had not contacted family or friends.
Detective Inspector Mark Benefield, the officer in charge of the investigation into Ms Thomas' disappearance, said today the arrest came after several weeks of hard work.
"We've made huge progress but we have got a long way to go yet to fully resolve this matter and we're determined to do so.
"I promised Carmen's mother I would do all I could to find her and I will do my best to keep that promise.
I spoke with her this morning to advise her of our activities."
The arrest came a day after it was revealed the investigation team had lowered a camera down a hole in a central Auckland construction site.
Officers spent part of yesterday morning visiting premises in Victoria St asking owners if they had seen anything suspicious and if they had any security camera footage from around July 1.
A worker at the construction site, who did not wish to be identified, told NZPA police had last week drilled a hole in a concreted area at the site, and returned today with a camera, which they lowered down the hole.
Mr Benefield said police were currently executing search warrants at residential and business addresses in Auckland.
He said he couldn't rule out the possibility of further arrests and charges at some stage.
"We don't know where Carmen is and we don't know how many people have been involved in her demise along the way," he said.
"We have recovered several items of interest to the investigation over the past 10 weeks and many have been submitted for forensic examination.
"It is vital that anyone who has information about where Carmen is comes to us directly and gives us that information.
She has a son and other family members who, along with us, want to ensure she is finally given a dignified resting place."
At the weekend, police confirmed they had found Ms Thomas's recycling wheelie bin on September 1, which had been missing from her Remuera home.
The bin was forensically tested, as was her car, which was found with blood inside on a Hamilton street in July.
