According to the analyst firm, this is a complete reversal from the first half of 2008, when less than 10 percent of netbooks shipped with Microsoft's operating system.
"Not only are people overwhelmingly buying Windows, but those that try Linux are often returning it," said Microsoft's Brandon LeBlanc in response to the NPD figures.
"Both MSI -- a leading netbook PC OEM -- and Canonical -- the vendor supporting the commercial distribution of Ubuntu Linux -- stated publicly they saw Linux return rates four times higher than Windows," LeBlanc added.
LeBlanc also claimed that consumers were choosing Windows because "it's easier to use, just works out of the box with people's stuff, and ultimately offers more choice".
Microsoft also revealed that it plans to put its forthcoming Windows 7 operating system onto netbooks.
"We've been testing Windows 7 on netbook PCs since before Windows 7 was feature complete, and our plan is to enable these small notebook PCs to run any edition of Windows 7".
See all netbook review
See also: Netbooks killing Microsoft's profits
This story, "Windows Dominates Netbooks" was originally published by PC Advisor (UK).