The software giant found itself embroiled in a race row after the doctored photo was found on its Polish website.
The doctored image, showing three workers sitting around a conference table, featured a white man's head with the black hands of the man that he replaced.
It appeared in its original form on Microsoft's US website.
Microsoft has apologised for the incident and taken the offending image down.
A spokesman said: "The image has been removed. Diversity and inclusion are core values and business imperatives of Microsoft and we apologise for any offence that might have been taken."
Microsoft said it would be investigating who made the changes.
The images have been circulating online, making the rounds on Twitter and various blogging websites.
A writer from the Photoshop Disasters blog said: "I think the intention was to make this ad even more PC, since you now have an Asian guy, a woman and a black guy's body with a white guy's head. When you can't add more people, fuse them together!"
