The incident occurred on Sunday in the first round of the tournament after the match had ended and the boy climbed down from the stands to snap a court-side picture with the 17-time Grand Slam champion using his smartphone.
“This should never happen on the Philippe Chatrier court,” Federer said, complaining of the lack of security.
“I’m not happy about it — obviously, not one second I’m happy about it.”
It happened as Federer was walking off the court after beating Columbia’s Alejandro Falla 6-3, 6-3, 6-4.
But Froome suggested in a tweet that Federer should learn to live with such intrusions.
"Harden up," the 2013 Tour de France winner tweeted with a picture of what he has to put up with from fans in cycling races.
“Wonder what RF would have to say about ASO security on Alpe d’Huez?” Froome said in another tweet.
“Give me a couple of kids wanting selfies any time.”
Federer said he generally had no problem with selfies, saying that he posed for several every day.
His concern was with security on the court and “we want players to feel safe”.
He noted that a similar incident happened when he was practising.
“On centre court, where you would think this is a place where nobody can come on, he (the boy with the smartphone) just comes on and nothing happens.”
Federer said he was not just speaking for himself but on behalf of all players.
French Open tournament director Gilbert Ysern said the incident was embarrassing but there was no need to change security procedures.
“It was just a lack of judgment,” Ysem said, the BBC reported.
“Clearly, the security people who were on court did not do the job the way they should have done, of course, to say the least,” he said.
“But it’s not the end of the world.”
Tournament organizers also rubbed Federer’s fellow countryman Stan Wawrinka the wrong way by publishing an article on the Roland Garros website that talked about his private life.
Wawrinka has recently separated from his wife.
The 2014 Australian Open champion said he saw the article on Saturday and immediately communicated his unhappiness to tournament officials.
Wawrinka said it was a “completely stupid article”, which was subsequently removed from the tournament’s website.
"It's the official website of a Grand Slam, so I hope the guy who did that article is not a journalist," Wawrinka said, according to a report from Associated Press.
"I also hope the guy who is supposed to check all the articles on the website is not working anymore for the tournament."