The governing body said a medical swab taken from the 28-year-old came back again as positive on Wednesday, which is expected to rule the player out of Liverpool’s match with Leicester in the Premier League on Sunday.
Salah, who initially tested positive for coronavirus on Friday, has missed Egypt’s Africa Cup of Nations qualifiers against Togo on Saturday and Tuesday.
“Today, Mohamed Salah, the star of the national team and the English club Liverpool, made a new swab to detect the Covid-19 virus, but its result was positive,” a statement from the Egyptian FA read.
UK government coronavirus rules dictate individuals must undergo a 10-day isolation period after a positive test.
It is unclear whether Salah will be allowed to travel back to the UK on Monday, once the enforced period of isolation ends, or whether he has to test negative before he can.
Salah is the fourth Liverpool first-team player to test positive for coronavirus this season, following Thiago in September and then Sadio Mane and Xherdan Shaqiri in October.
Liverpool are without long-term absentees Virgil van Dijk and Joe Gomez, while right-back Trent Alexander-Arnold is also sidelined through injury.
Captain Jordan Henderson withdrew from the England squad for their Nations League match against Iceland on Wednesday.