Housing Minister Phil Heatley's Wellington residence costs $15,838 more than the new annual allowance, meaning he has to move to stay within the budget or pay the extra from his own pocket.
Mr Heatley yesterday acknowledged he would lose under the new system, but said: "We'll make it work".
A Herald analysis shows Mr Heatley's ministerial accommodation costs the taxpayer $53,338 a year.
But under the system set up by Prime Minister John Key, Mr Heatley will receive a $37,500 lump sum for accommodation.
He said he would talk to his wife Jenny about whether they would keep the property they were in, and did not mind digging into his own pocket.
Mr Heatley moved into the taxpayer-funded home when he became a minister and rented the apartment he had lived in as an Opposition MP to one of his National colleagues, for which the taxpayer also picked up the bill.
Unlike some other ministers, he had a young family he wanted to live with him in Wellington.
"I'm in the situation where I've got three children. That's fine - I'm just going to deal with it and move on."
Police Minister Judith Collins' accommodation costs $6898 more than the allowance.
Asked about her reaction to Mr Key's decision, she replied: "I am happy to be a member of John Key's Government."
Under the new system, ministers will be able to pocket any of the taxpayer money they don't spend.
The Herald analysis shows ministers Jonathan Coleman, Tim Groser, Wayne Mapp, John Carter, Pansy Wong and Georgina te Heuheu will gain.
Labour raised concerns that ministers could seek cheap accommodation to get a tax-free addition to their salary.
Labour leader Phil Goff said the money paid should be based on actual costs, with receipts for rent and utilities provided to prove the system was not being cheated.
Mr Goff said it was harder for MPs to provide receipts for the $14,000 allowance they get for expenses, which covered a wide range of expenditure such as donations in the street.
WINNERS AND LOSERS
OVER-BUDGET
* Housing Minister Phil Heatley: set to spend $53,338 this year, $15,838 over the new $37,500 allowance.
* Police Minister Judith Collins: $6898 over.
SET TO PROFIT
* Immigration Minister Jonathan Coleman: set to spend $7062 less than allowance - that will be his under the new regime.
* Trade Minister Tim Groser: currently $5226 under.
* Herald analysis is based on the ministerial and parliamentary accommodation expenses for the first six months, multiplied to get an annual figure.
Key's allowance change takes $15,838 out of minister's pocket
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