Manaudou made her comments shortly after news broke of the Toulouse shootings which killed a teacher and three children on Monday.
She wrote "get rid of these video games and things will improve."
She then added "yes, I'm referring to Toulouse … not only are there fools around but the fact they attack Jews is really disgraceful."
Her tweets attracted a number of negative and sarcastic comments and came just as the 25-year-old was racing to win a place in the French swim team for this year's Olympic Games.
"For me, until now, everything was great and people were great" she said on Monday after closing her account. "Apparently not. It's definitely affected me. I didn't expect it. I'd rather leave Twitter than read negative things about me."
On Tuesday, Manaudou won her place in the Olympic team after winning the 100 metres backstroke final in the French championships.
Her boyfriend, Frédérick Bousquet, also a swimmer, tweeted on the same day "my sweetheart is back on Twitter."
Manaudou has since set up a new Twitter account under the name @Manaudou and, by Wednesday morning, had already gained 2,000 followers.
Manaudou won the gold medal in the 400-metre freestyle in the 2004 Athens OIympics, although finished last when she tried to repeat her success in the 2008 Beijing Games.
She retired from competitive swimming in 2009 and gave birth to a baby in 2010.
She announced her intention to return to swimming in July 2011 and is looking to recapture her past form at the London Olympic Games due to start on July 27th.