Steven Joyce says the payroll problem in his ministry is "annoying and concerning" but it's nothing like the Novopay debacle.
"It goes back several years, possibly more than a decade," the business, innovation and employment minister told NZ Newswire.
"It's mostly about holiday pay, it's relatively minor on an employee to employee basis but could add up to something more significant across the whole agency."
Mr Joyce says the total amount involved isn't yet known, nor is it known how many of MBIE's 3300 staff are affected.
MBIE's problems were revealed by media last night.
The ministry's chief financial officer, Stewart McRobie, was quoted as saying the issue would be resolved as quickly as possible.
Mr Joyce was the minister called in to sort out the Ministry of Education's Novopay system when it went seriously wrong after being launched in August 2012.
He says his own ministry's issues are "nothing like that" and he'll receive a report in a few weeks on how the problem is being tackled.
"My experience in these matters is that if you start to move on it before you have a clear understanding of exactly what you need to do, there is always potential to make the situation worse."
Labour's economic development spokesman, David Clark, says millions of dollars could be involved and the buck stops with Mr Joyce.
"It is a fundamental part of any organisation to be able to pay its staff properly," he said.
"That MBIE can't pay employees effectively is deeply embarrassing - this goes straight to Mr Joyce as the minister responsible."