The company, called SenseNets, sells facial recognition and crowd analysis technology that is designed to detect unusual behavior in large groups of people, according to its website.
SenseNets suffered a data leak in February which was discovered by security researcher Victor Gevers. He revealed that personal information on 2.5 million people tracked by the company was publicly available. Gevers found that most of the records were collected in China's Xinjiang province, a region in the west of China with a large population of minority Uighur Muslims.
Various rights groups have urged the United Nations to carry out a fact-finding mission in Xinjiang. The U.S. State Department weighed in on Thursday on China's human rights violations against Muslims in Xinjiang, calling it "great shame for humanity."
The Chinese government has consistently denied any wrongdoing with regard to the Uighurs.
SenseNets did not respond to three attempts by CNBC this week to contact the company.
Reports suggest that facial recognition is part of a wide-scale surveillance program in the region that also includes the collection of people's DNA samples.
SenseNets, which is involved in the facial recognition aspect of the program, lists Microsoft on its website under its "partners" section.
The U.S. software giant denied any involvement with the company.
"Microsoft is not involved in a partnership with SenseNets. We have been made aware SenseNets is using our logo on its website without our permission, and we have asked for it to be removed," a spokesperson for the company told CNBC on Friday.
Microsoft sells software for facial recognition based on its cloud product Azure. Third parties can purchase Microsoft's software for use in their own applications. But Microsoft said it has no relationship with SenseNets.
The company's denial comes after Gevers posted a screenshot of code from SenseNets software. It shows a line of code appearing to be tied to Microsoft's facial recognition tool.
Gevers told CNBC on Friday that the Microsoft code could have been present because an individual developer brought it and paid for it themselves or used a free trial. This means there would be no trace back to SenseNets.
CNBC asked Microsoft to clarify whether SenseNets could have access to its tool without paying for it or without the company's knowledge. Microsoft did not immediately respond to that inquiry.
Microsoft has tried to lead the responsible development of artificial intelligence.
In January, CEO Satya Nadella called for regulation on facial recognition technology. Microsoft has a six-point manifesto that it says guides its facial recognition work. One of those points is "lawful surveillance," in which it advocates for "safeguards for people's democratic freedoms in law enforcement surveillance scenarios."
Microsoft has said it will "not deploy facial recognition technology in scenarios that we believe will put these freedoms at risk."