Companies like Facebook, Google Inc. GOOGL -0.03% and Twitter Inc. TWTR -0.02%rely almost solely on data-driven advertising dollars. As a result, the companies collect and store massive amounts of personal information. Not all of that information can be used for advertising—at least not yet. In the case of Facebook, there is an abundance of information practically overflowing from its servers. What Facebook does with all its extra personal information—the data isn't currently allocated to the advertising product—is largely unknown to the public.

Facebook's Data Science team occasionally uses the information to highlight current events. Recently, it employed it to determine how many people were visiting Brazil for the World Cup. In February, The Wall Street Journal published a story on the best places to be single in the U.S., based on data gathered by the company's Data Science Team.

Those studies have raised few eyebrows. The attempt to manipulate users' emotions, however, struck a nerve.

"It's completely unacceptable for the terms of service to force everybody on Facebook to participate in experiments," said Kate Crawford, visiting professor at MIT's Center for Civic Media and principal researcher at Microsoft Research.

Ms. Crawford said it points to broader problem in the data science industry. Ethics are not "a major part of the education of data scientists and it clearly needs to be," she said.

Asked a Forbes.com blogger: "Is it okay for Facebook to play mind games with us for science? It's a cool finding, but manipulating unknowing users' emotional states to get there puts Facebook's big toe on that creepy line."

Slate.com called the experiment "unethical" and said "Facebook intentionally made thousands upon thousands of people sad."

Mr. Kramer defended the ethics of the project. He apologized for wording in the published study that he said might have made the experiment seem sinister. "And at the end of the day, the actual impact on people in the experiment was the minimal amount to statistically detect it," he wrote on Facebook.

Facebook also said the study was conducted anonymously, so researchers could not learn the names of the research subjects.

Mr. Kramer said that the content—both positive and negative—that was removed from some users' news feeds might have reappeared later.

The emotional changes in the research subjects was small. For instance, people who saw fewer positive posts only reduced the number of their own positive posts by a tenth of a percent.

Comments from Facebook users poured in Sunday evening on Mr. Kramer's Facebook page. The comments were wide-ranging, from people who had no problem with the content, to those who thought Facebook should respond by donating money to help people who struggle with mental health issues.

"I appreciate the statement," one user wrote. "But emotional manipulation is emotional manipulation, no matter how small of a sample it affected."

Facebook users agree to terms of service that give the company wide leeway in how it can treat them.

Write to Reed Albergotti at reed.albergotti@wsj.com