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The pair, aged 29 and 58, were arrested by police at Christchurch Airport on Monday night, police said.
The 29-year-old faces two charges under the Immigration Act, after allegedly assisting a wanted person to leave the country.
The 58-year-old has been charged in relation to obtaining by deception and using a forged document.
Customs Minister Kris Faafoi called the Customs episode a "human error which shouldn't have happened".
Customs, at the time, said it was reviewing its processes and Faafoi said he had been reassured it was an exceptionally rare occurrence.
Two other people, arrested separately in February, were also charged over the roofing scams.
An 82-year-old Auckland woman is one of the complainants after allegedly being scammed out of almost $9000.
Greenlane resident Heidrun Leonard said the supposed tradesmen knocked on her door on January 4, saying they had noticed from the street there was a leak in her roof that needed repairs.
"You have to give us $8800, and once we have done the job, you will get the $8800 back," Leonard said the men told her.
She wrote the cheque they then cashed at the bank.
The next morning they came back to her house and cut a rectangular hole in her ceiling, before fleeing when Leonard's neighbour arrived and began asking questions.