The 17-time Grand Slam winner had just completed a routine 6-3, 6-3, 6-4 win over Colombia's Alejandro Falla when he was shocked to see a young fan sprinting towards him on the showpiece Philippe Chatrier Court.
It was particularly embarrassing as security at this year's French Open has been tightened following January's deadly Islamist attack on Paris-based satirical magazine Charlie Hebdo.
Although the male fan was quickly manhandled away, 33-year-old Federer was furious with the lapse in security, claiming he had also been targetted in practice on Saturday.
"Something needs to happen quickly. 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.
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"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."
Two years ago the final, which featured Rafael Nadal, was also held up when a shirtless spectator, brandishing a flare, leapt from the stands and onto the court before he was wrestled away by security officials. Player safety at tennis tournaments has been a major concern ever since 1993 when Monica Seles was stabbed by a deranged fan in Hamburg.
Tournament director Gilbert Ysern admitted that Federer was right to be "pissed off" and admitted that the youth, who had been sitting in the courtside sponsors boxes, had been banned from the event.
Federer, the 2009 champion and seeded two this year, goes on to face Spain's Marcel Granollers for a place in the last 32. Federer, one of a record 39 men over 30 in the first round, is desperate to make the most of a kind draw which dumped top seed Novak Djokovic, nine-time champion Rafael Nadal and third seed Andy Murray all in the opposite half.