He said he felt for the organisation because it had a lot of tremendously good people in it.
"But one or two people have really let that organisation down badly.
"I think there will be an awful lot of people in MFAT, whatever they think of the process and whatever they think of the outcome, will be ashamed at their organisation as a result of that."
He said while he had sympathy for people who were going to lose their jobs in the restructuring "but in the end when you come into an organisation like a Government department then you have a responsibility to act professionally and whoever has leaked that information hasn't."
Mr Key said his own experience of MFAT staffers was that they were "hugely professional."
Foreign Minister Murray McCully is overseas in the Middle East and so no final decisions are expected to be made this week.
Asked if the restructuring had been botched, Mr Key said the Government had made a lot of changes in the past three and a half years and generally speaking it had gone smoothly.
"And whatever way you define this, this hasn't, and we need to learn some lessons from that."