The Swiss appeared startled as the fan appeared on court as Federer walked off having defeated Alejandro Falla in straights sets. Security staff then whisked the offender away.
Security at the tournament was breached two years ago during the final between Rafa Nadal and fellow Spaniard David Ferrer when a protestor leapt from the stands on to the court, carrying a flare and protesting against France's same-sex marriage law.
"I'm not happy about it. Obviously not one second I'm happy about it. It happened yesterday in the practice, too," Federer told reporters.
"It's just a kid, but then three more kids came. And today on center court where you would think this is a place where nobody can come on, he just wanders on and nothing happens."
Federer added that tournament director Gilbert Ysern had apologized to him.
A boy who climbed down from the stands runs to get a selfie with Switzerland's Roger Federer in the first round match of the French Open tennis tournament against Colombia's Alejandro Falla at the Roland Garros stadium (AP Photo/David Vincent) Source: AP
"It happened during the finals in '09 as well for me. So I definitely think this is something that something needs to happen quickly. Basically yesterday already.
"Normally I only speak on behalf of myself, but in this situation I think I can speak on behalf of all the players, that that's where you do your job, that's where you want to feel safe. And so clearly I'm not happy about it.
"But nothing happened, so I'm relieved. But clearly it wasn't a nice situation to be in."
Ysern told a news conference that even though a mistake had been made and that the incident was "embarrassing", there was no reason to change security procedures at the tournament.
"It was just a lack of judgment this afternoon. 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.
Security has been upped in France after fatal terror attacks in Paris in January, but Ysern added there is nothing organizers could do if hundreds of fans were to invade the court.
(AP) Source: AP
Former Tour de France champion Chris Froome, who is used to riding through thousands of fans during cycling races, ribbed Federer, tweeting: "Harden up, Roger Federer."
He also wrote: "Give me a couple of kids wanting selfies anytime."
In 1993, former women's world number one Monica Seles was stabbed in the back on court during her quarter-final match against Bulgarian Magdalena Maleeva in Hamburg.
"We need to make sure that it's safe out there and people don't just wander on the court like a free pass, you know. That's how it's supposed to be," said Federer.
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