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Foreign Minister Murray McCully was searched at Auckland Airport before flying out to the United States last month.
The random search is reported to have been carried out at the request of the US and happened despite Mr McCully travelling on a diplomatic passport.
A spokeswoman for Mr McCully said the search was the result of an "administrative error".
"Due to an administrative error in New Zealand the Minister was subject to a random search before departing for Washington. The Minister was not screened in the United States."
The search was at the request of the United States, Radio New Zealand reported today.
Mr McCully was flying to Washington on March 21 for a meeting on fighting Isis.
He is stepping down as Foreign Minister, a role he has held for eight years.
On Monday, Prime Minister Bill English announced that Gerry Brownlee would be the new Foreign Minister.