It shows that despite Gordon Brown's pledge to give pound;300 million directly to headteachers, most are facing shortfalls this year of up to pound;500,000.
At the most extreme, 6 per cent of heads complained they were at least pound;250,000 short. A fifth said they needed pound;90,000 or more to cover repairs, staffing and books.
The survey was commissioned after last week's pound;1 billion Budget boost for education, which gave primaries with more than 200 pupils an extra pound;9,000 and secondaries of 1,200-plus pupils, pound;50,000.
It comes as the House of Commons Library statisticians revealed that Labour will not meet its manifesto pledge to increase the share of national wealth spent on education to 5 per cent by the next election.
NOP pollsters commissioned by The TES and BT Education asked 200 heads how they would spend an extra pound;50,000.
Top of their shopping lists were staff - both teachers and support - and coputers. Close behind were books (53 per cent) and building repairs (41 per cent). Almost one in five said they would spend cash on sports equipment.
The primaries taking part averaged 232 pupils and would qualify for the maximum pound;9,000 Budget grant while the secondaries averaged 1,047 pupils, qualifying for pound;40,000.
The findings disturbed head-teacher unions who feared one-off windfalls for schools were being used to provide short-term solutions to long-term problems.
David Hart, general secretary of the National Association of Head Teachers, added: "You can't take on permanent staff on the basis of a one-year grant.
"All this adds to the pressure on Government to do something much more dramatic about the way we fund schools. We need a national funding formula."
Jim Moore, general manager of BT Education, said: "Clearly this research shows that the need for more teaching staff remains the major issue for headteachers.
"However, the results of the survey also underline the increasingly important role ICT is playing in both primary and secondary schools."