For one week in 2012, the social media giant intentionally put upbeat posts on some of its users' feeds and negative posts on others.
It was part of a psychological study Facebook conducted with researchers at Cornell and the University of California, San Francisco.
Many online expressed outrage after learning about the study, which focused on 690,000 users.
There is no indication that the subjects were asked if they would like to take part in the study.
One of the Facebook researchers who designed the experiment published a post Sunday apologizing.
A spokesman for the company said the company frequently does research to improve the site's content and that they never collect unnecessary information.
The study found people who got bad news were slightly more likely to write negative posts while those who heard good news responded more positively.
The results of the study were published this month in the journal Science.