Lower-paid classroom teachers in England and Wales are to receive pay rises of up to 3.5%.
But the Institute for Fiscal Studies said that about 60% of teachers and senior staff will get below-inflation increases of 1.5% or 2%.
Schools in England will receive £508m to cover the increases, from existing Department for Education budgets.
"There are no great schools without great teachers," said Education Secretary Damian Hinds.
He said the pay rises would help teaching to be a "competitively rewarded career".
'Back of the departmental sofa'
The government has announced tiered increases, accompanied by funding grants for schools - rather than implementing the independent teachers' pay body's call for an across-the-board 3.5% increase.
Geoff Barton, leader of the ASCL head teachers' union, said the pay increase was "only partially funded" and a "short-term political solution" using money "from down the back of the departmental sofa".
Paul Whiteman, leader of the National Association of Head Teachers, said those staff getting below-inflation deals of 1.5% and 2% would "feel very let down" as they were getting a "real-terms pay cut".
The teachers' pay deal will see 3.5% rises - worth between £800 and £1,366 per year - for many classroom teachers on the main pay range.
It marks the biggest pay rises for school staff since the introduction of public sector pay restraint, as part of austerity measures in the wake of the financial crash a decade ago.
There will be lower increases of 1.5% and 2% for higher-paid teachers, senior staff and head teachers.
The IFS analysis of the pay rise says that about 60% of staff will receive these "below-inflation awards".
Starting salaries for new teachers outside London are about £23,000, with average pay for teachers £38,700.
However, teachers in the middle of the main pay scale will be earning about £10,000 a year less than this figure.
Mary Bousted, leader of the National Education Union, said they would "continue to campaign" for an across the board increase.
Chris Keates, leader of the Nasuwt teachers' union, said the announcement would "raise expectations of a pay award but will fail to deliver one for all teachers".
Schools in England will receive £187m and £321m over the next two years to pay for the increases - but the DFE has so far not given details of whether there will be cuts elsewhere to fund this.
This funding to support the pay rise will not apply to schools in Wales - and the Welsh government said it was "concerned that HM Treasury will not be providing any additional funding to pay for this uplift".
Head teachers had warned that an unfunded pay increase would have been "catastrophic" for already stretched school budgets.
They had written to the education secretary to say that it would have made schools effectively insolvent.
But the Department for Education says that its extra funding makes the pay rises "fully affordable" to schools and will not add to the financial pressures.
A pay rise has been seen as important to tackle a teacher shortage - with Mr Hinds saying that improving recruitment was a top priority.
But schools have been protesting about budget shortages, with the Institute for Fiscal Studies reporting that per pupil spending had fallen by 8% in real terms.
Head teacher Jules White, who has campaigned against school funding shortages, said schools will have to "raid their already devastated budgets to fund part of the increase".
Labour's shadow education Secretary Angela Rayner said for some teachers it would mean "another real terms pay cut for the eighth year in a row".
"There is still no information about what areas of funding will be cut to meet the cost of the pay rise," said Ms Rayner
Education Secretary Damian Hinds said: "I want us to recruit and retain brilliant teachers who are fairly rewarded for the vital work they do".