Meilutyte is the world record holder and reigning world champion in 50 metres (m) breaststroke, which is not held at the Olympics, and won 100m gold at London 2012 as a 15-year-old.
She was 100m world champion in 2023 but failed to reach the semi-finals at last month's world championships in Doha.
The federation said on their website, opens new tab that Meilutyte had undergone surgery in Kaunas after returning from Qatar.
"Ruta's foot has been hurting for several months during heavy physical exertion. After carrying out the tests, we found damage to the first metatarsal bone of the left foot," it quoted orthopaedic surgeon Gintautas Pocius as saying.
"Since the operation is a minimally invasive arthroscopy, we expect a quick rehabilitation process."
The federation said Meilutyte would have to wear a special brace for three weeks. "The procedure will not disrupt the normal preparation plan for the Paris Olympics.
In any case, a two-to-three week rest is planned after the world championships in Doha," it added.
The Paris Olympics open on July 26.
--Reuters--