Taxpayers earning more than $80,000 are set to get their promised tax cuts from October, but only after a backdown by the bureaucracy.

After the $6 per week tax cut was announced in the May budget, Tax Commissioner Chris Jordan defied Prime Minister Malcolm Turnbull who said it would be implemented "administratively" because the Parliament wouldn't be able to sit before it was due to start on July 1.

Mr Jordan told the Treasury and Finance departments that he wanted "the relevant legislation to be passed before the change will be incorporated into the income tax withholding schedules".

This meant that although high earners might eventually get a refund of up to $6 per week, tax would be deducted from their pay packets at the old rate until the legislation had been approved by both houses of Parliament.