Investigators from the State Administration for Industry & Commerce (SAIC) said that the company must abide by Chinese law, and shall not interfere with the investigation "in any way", state-run Xinhua news agency reported.
SAIC confirmed that it launched a probe into Microsoft China Co Ltd, and three of its branches in Shanghai, Guangzhou and Chengdu as the firm is suspected of monopoly practices.
According to SAIC, in June last year, it investigated complaints from enterprises that Microsoft used tie-in sales and verification codes in its Windows operating system and Microsoft Office software suite, practices that may have breached China's anti-monopoly law.
SAIC also said the company did not fully disclose information of its products, as required by law, causing software incompatibility issues.
Inspectors said last week they had made copies of the firm's financial statements and contracts and seized documents, e-mails and other data from computers and servers, but they had not been able to complete the investigation because key personnel of Microsoft were not in China or could not be reached.
Microsoft Corp's China unit responded on Wednesday saying it has always abided by laws and regulations in China and will "actively answer" questions raised in the anti-monopoly case.
Despite the probe, the US company said last week that its Xbox One games console will come on to the Chinese market on September 23.
It will be the first games console legally available in China since a ban on the gaming sector in 2000.
In May, China announced it would ban government use of Windows 8, Microsoft's latest operating system, because of suspicions about cloud technology that stores key information elsewhere.