Ministers have criticised the decision to break the public sector pay cap by handing MPs a 1.3% rise this year.
The Independent Parliamentary Standards Authority (Ipsa) has confirmed that the increase will take effect from next month - less than a year after politicians received a back-dated 10% hike to £74,000.
By contrast workers such as NHS staff and members of the armed forces have been limited to 1%.
In a letter to Commons Speaker John Bercow, Chief Secretary to the Treasury Greg Hands stressed that he recognised the watchdog's independence.
But he added: "The Government's policy is for public sector pay to increase by 1% per year, and its position on increases in MPs' pay, at a time when difficult decisions are being taken elsewhere to reduce the deficit, has not changed.
"The part of MPs' pay we do control - ministerial pay - has been frozen until 2020."
Under the pay package introduced by Ipsa, MPs salaries are uprated annually in line with increases in average weekly public sector earnings.
However, those figures are typically higher than the 1% cap because they include bonuses and promotions.
Downing Street previously said the rises were a "matter for Ipsa" and were automatically paid to all MPs.