Mr Matthews assured the committee there had been changes made to prevent future errors.
"With the NZTA, we commissioned a major review of the cash management processes end to end since then, and they have now been significantly strengthened."
Speaking to APNZ outside the committee, Mr Matthews said he could not remember the date the error was made, but said the ministry had caught it six months later.
"What it meant was that, because the agency thought it had more money for a while, it was able to anticipate that it could do more than it could," he said.
While none of the money was spent and the mistake had only affected planning, Mr Matthews said the ministry was not resiling from the seriousness of the error.
"We were quite transparent about it when it occurred, we put our hands up and said 'this accounting error has occurred, it's been fixed' ... and as I say, that staff member resigned."