It's hoped a diplomat will be appointed MFAT's new boss, as its embattled chief executive steps down.

John Allen's leaving for the New Zealand Racing Board after five years at the ministry.

He oversaw a botched restructuring process and the Malaysian diplomat scandal.

Mr Allen lacked a foreign affairs background - and Labour's David Shearer says it's important an MFAT insider replaces him.

"The Ministry is micro-managed by Murray McCulley, he will be wanting someone who will follow his instructions, but with New Zealand on the Security Council for the next two years, it's got to be someone with some pretty serious background in foreign affairs."