A report by the UK's education and IT watchdog suggests schools could save money by shopping around for software.
Software costs could be cut, Becta said
Research by Becta (British Educational Communications and Technology Agency) found schools could make savings if they used non-proprietary software.
The report did not name Microsoft directly, but the company is one of the largest suppliers of software to British schools.
Microsoft has said the survey was based on too few schools to be conclusive.
The report said primary schools could save up to 50% and secondary schools more than 20% if they switched to what is known as "open source software".
"The potential cost benefits and savings clearly make it an option worth serious consideration," it said.
Researchers surveyed 33 schools using proprietary software and compared them with 15 schools that had moved to open source systems.
In open source software, the underlying computer code is made freely available so users can alter it and publish new versions, the aim being to benefit the community at large.
Owen Lynch, chief executive of Becta, said: "There are many factors that determine the true cost of products and services. The cost of support, training and maintenance, and reliability issues, are as important as the purchase price when considering the total cost of owning and using technology.
"This report indicates that open source software can provide a cost-effective and efficient solution in schools if effectively deployed. Becta believes that software used in schools should be of a high quality and adhere to open standards, enabling compatibility and interoperability between products."
He said Becta would now be undertaking more extensive research across a wider range of institutions to allow further analysis of these issues.
Microsoft signed a new licensing deal with Becta, acting on behalf of the British government, in December.
The company says it has been cutting its prices to Becta.
Stephen Uden, group manager of education relations at Microsoft UK said: "It costs about 20% for schools to buy software, compared to the cost to business".
And he said the survey sample was small: "There's about 30,000 schools in the country, this report looks at 15," he said.
"It's really difficult to draw big conclusions from such a small sample."
The average amount spent by secondary schools on information technology last year was £88,200 - up from £65,000 in 2003, according to figures released by the Department for Education and Skills (DfES) in January.
The average figure for primary schools was £18,500.