Labour MP Phil Goff questioned Mr Allen - during a tetchy hearing at Parliament's foreign affairs select committee - about the state of the ministry following the restructuring.
In his opening statement to the committee, Mr Allen said the ministry had had a year of which it could be proud.
But Mr Goff said staff turnover had trebled and only 15% of ministry staff felt engaged.
Mr Allen rejected suggestions that staff felt that way.
Mr Goff said the chief executive was simply defending his minister, Murray McCully, who was behind the restructuring.
He questioned why Mr Allen got a pay increase of $40,000 when the restructuring at the ministry was badly handled.