Research by TechCrunch found that the volunteers for the scheme had been paid up to $20 a month in return for opening up their phones to analysis.
However, Facebook has rubbished the accusation of spying, saying it was an unfair and inaccurate characterisation of the situation.
A spokesperson for the company explained: "Key facts about this market research program are being ignored.
"Despite early reports, there was nothing 'secret' about this; it was literally called the Facebook Research App. It wasn't 'spying' as all of the people who signed up to participate went through a clear on-boarding process asking for their permission and were paid to participate.
"Finally, less than five percent of the people who chose to participate in this market research program were teens. All of them with signed parental consent forms."
Facebook has also stressed that its market research policies are not unusual.
The social networking platform said: "Like many companies, we invite people to participate in research that helps us identify things we can be doing better.
"Since this research is aimed at helping Facebook understand how people use their mobile devices, we've provided extensive information about the type of data we collect and how they can participate.
"We don't share this information with others and people can stop participating at any time."