"Although this subject matter was important to research, we were unprepared for the reaction the paper received when it was published and have taken to heart the comments and criticism," Schroepfer said. "It is clear now that there are things we should have done differently."

He said the Menlo Park, Calif., company should have considered other non-experimental ways to do the research, and that the research would also have benefited from more extensive review by a wider and more senior group of people. He also conceded that Facebook "failed to communicate clearly why and how we did it."

Schroepfer also explained that Facebook decided to do the study after separate research in 2011 suggested that when people saw positive posts from friends on Facebook, it made them feel bad. He said the company wanted to see if that assertion was valid to "see if there was anything we should change about Facebook."

"We want to do this research in a way that honors the trust you put in us by using Facebook every day," Schroepfer said. "We will continue to learn and improve as we work toward this goal."

Twitter: @byandreachang