The Remuneration Authority says a pay rise of just over 2% for MPs was lower than it could have chosen, because of the need to restrain public sector expenditure.
The Prime Minister will now get $428,500 a year, a $9200 increase.
His deputy Bill English receives a $6500 rise taking his pay to $303,900.
The pay for backbench MPs goes up from $144,600 thousand to $147,800.
In its determination on Thursday, the authority said it appeared the pay rates of the Prime Minister, his deputy and ministers were falling behind market rates and it will review that gap in the coming year.
Many ministers and MPs leaving on Thursday for the parliamentary recess would not comment on the pay rises - some saying it is never a good news story.
Labour MP Annette King said having an independent body setting MPs salaries is absolutely the right way to go, because the public needs to be assured that MPs aren't hiking their own pay.
National's Paul Foster-Bell said in real terms the payrise is less than 2% because the travel entitlement has been reduced slightly.
The increase is backdated to July, and Labour MP Grant Robertson says it would be good if the determination was made a bit earlier to avoid backpayments.