He told media afterwards that he had not considered turning the pay increase down.
"It didn't enter my mind at all because it had been through a performance management process with the State Services Commission, because I knew that process was robust and I thought as a consequence of that it was appropriate to accept the increase."
He did not think it was a bad look to take the increase, saying the changes at Mfat were necessary and beneficial for New Zealand.
The changes at Mfat followed a major review earlier this year but the original proposed savings had to be watered down after a public revolt by usually strictly non-partisan diplomats and intervention by Minister Murray McCully. Mr Goff and media received several leaks from Mfat staff at the time.
Yesterday Mr Allen said a State Services Commission-led investigation by Paula Rebstock into those leaks was still underway, but he believed the days of leaks were over.
"The fact there were some leaks simply reflects the fact that there were a very small number of people who felt so passionately about some of the elements of the change that they felt that was appropriate. It wasn't, it isn't and you'll have noted the ministry is not now leaking."
Mr Allen said those changes were necessary and claimed the ministry was now more flexible and modern, and its people were "proud and confident of the future."
In the committee, he disputed Mr Goff's claims that changes to conditions and allowances had made it hard to recruit and keep good diplomats, saying there was still healthy competition for overseas postings and some staff were better off as a result.
Mr Allen also defended an increase in the staff turn-over at Mfat from about 5 per cent to 13 per cent since the restructure, saying it was in line with other public sector organisations and was to be expected after a major review. Many of those who had left had worked in roles such as IT or human resources, rather than diplomats.
Problems in morale which were reflected in a staff survey earlier this year were no longer an issue.
Mr Goff also asked Mr Allen to confirm whether 40 heads of missions - such as ambassadors or High Commissioners - had left Mfat since the restructure for reasons other than retirement.
Mr Allen said he did not know exact numbers, but was confident Mfat had sufficient talent at the senior, middle and junior levels to deliver results for Mfat.