It said a report from the British Educational Communications and Technology Agency released last week was based on a study of the technology costs at fewer than 50 schools and possible savings at just 15 schools that have pioneered the use of cut-price software, of which just six were primaries.
Stephen Uden, education relations manager for Microsoft UK, said: "It's really difficult to draw large conclusions from small samples of schools."
The report, previewed by The TES earlier this month, found that costs per computer were 44 per cent higher in primaries using Microsoft and other paid-for products rather than free or cut-price alternatives and 24 per cent higher in secondaries.
Most of the cheap software is "open source" meaning users can freely adapt the program code. Mr Uden said that, of the six primaries running open source, three were getting free technical support from a secondary.
But Vanessa Pittard, of Becta, said: "We are not making large conclusions from small samples. We are saying that the evidence suggests that open source is something that schools should be looking at. We stand by that."