Microsoft Deputy General Counsel Mary Snapp was in Beijing to meet with the SAIC on Monday, where the regulator warned Microsoft to not obstruct the probe.
But industry experts have questioned how exactly Microsoft is violating anti-trust regulations in China, where the size of its business is negligible.
The U.S. company has taken a public beating in China in recent months. It has been subject to wider scrutiny against U.S. technology firms in China in the wake of former U.S. National Security Agency contractor Edward Snowden's cyber espionage revelations.
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It has also seen its OneDrive cloud storage service disrupted in China, and had its latest Windows 8 operating system banned from being installed on the central government's new computers.
The Microsoft investigation comes amidst a spate of anti-trust probes against foreign firms in China, including mobile chipset maker Qualcomm and German car maker Daimler's luxury auto unit Mercedes-Benz.
China is intensifying efforts to bring companies into compliance with an anti-monopoly law enacted in 2008, having in recent years taken aim at industries as varied as milk powder and jewelry.
China on Wednesday said it will punish foreign car makers Audi, owned by Volkswagen, and Fiat's Chrysler as well as some 10 Japanese spare-part makers for anti-trust violations.
A number of multinational companies including Mead Johnson Nutrition and Danone have been slapped with substantial fines following similar investigations in the past.