In announcing their latest decision, the Remuneration Authority said it had been made according to criteria contained in the Remuneration Authority Act 1977.
Mr Key said that meant a law change was necessary.
The change will mean the only thing considered will be the average public sector pay increase for the previous year.
The new legislation will be backdated to July 1 2014, meaning the pay increase announced last week will not be awarded.
Last Thursday it was announced that MPs would get a pay rise of 5.5 per cent - which translates to a $8200 pay rise for backbench MPs.
The Remuneration Authority said that once a reduction in the travel entitlement was taken into account, MPs' pay packages would increase by 3.5 per cent.
Before today's action, Mr Key's salary would rise by $23,800 to $452,500.
Mr Key has previously said he was disappointed with the authority's decision.
That lead opposition leader Andrew Little to accuse the Prime Minister of "crying wolf", given he had not taken action for five years to make sure pay-rises were not large.