The four-month delay will occur because up-to-date information on how many teachers will be eligible is not available, it said.
The Department for Education and Skills has conceded that, with only three months to go until teachers were originally supposed to be paid, it remains undecided about how to distribute the cash to schools.
The revelation provoked protests from the National Union of Teachers, which believes staff should get their rises without delay.
Ministers aimed to put an end to arguments by reaching a deal two months ago with headteachers' leaders. Teachers who meet the criteria will see their salaries rise from pound;27,894 to pound;28,926.
A DFES consultation paper reveals that the Government knows the number of teachers each school has on the three grades for which the extra money is intended: the upper pay, leadership spine or advanced-skills teacher grade.
But it does not know how many are eligible for the awards. For example, teachers who reached the upper pay spine last year will not normally be considered for the extra performance pay until next year. Those moving schools will also throw out the current figures.
The DFES suggests either dividing up the pound;90 million it is giving to schools this year using the information it already has, or carrying out a survey of how many eligible staff each school has in September.
Headteachers' leaders and employers favour the latter. John Dunford, general secretary of the Secondary Heads Association, said: "The pay rise will be backdated anyway, so time is not essential here. The system will be difficult to run if the numbers are not right."
But Doug McAvoy, general secretary of the NUT, said: "Teachers have the right to be paid at the earliest possible opportunity. The survey is not necessarily going to be accurate and it will just get in the way of paying teachers earlier."
Experience pays in Wales, 12