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.
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.
Liverpool could be missing nine first-teamers against Leicester
Analysis by Sky Sports' Richard Morgan:
Jordan Henderson and Andy Robertson have now joined a lengthening list of players set to miss Liverpool's top-of-the-table clash with Leicester City at Anfield on Sunday night.
Henderson was withdrawn at half-time of England's 2-0 loss in Belgium on Sunday after experiencing tightness in a muscle, while Robertson missed Scotland's 1-0 defeat to Slovakia earlier that day with a tight hamstring.
The Liverpool captain will be assessed when he returns to England, while the Scotland skipper will also be monitored ahead of his country's Nations League tie in Israel on Wednesday making both doubts for the champions' match with the Premier League leaders this weekend.
All of which adds to the current problems facing Liverpool manager Jurgen Klopp, who found out on Friday that top scorer Mohamed Salah had tested positive for Covid-19 while on international duty with Egypt.
Klopp has already lost centre-backs Virgin van Dijk and Joe Gomez to long-term knee injuries, while Liverpool's defence will also be missing regular right-back Trent Alexander-Arnold due to a calf strain sustained in their last league outing at Man City.
Meanwhile, Liverpool may be unable to use versatile holding midfielder Fabinho as cover in defence against the Foxes, with the Brazilian still recovering from the hamstring strain he picked up against FC Midtjylland at the end of October.
All of which means that Klopp could be without his entire first-choice back four when the Premier League returns to action after the international break, with midfield also a problem area for the German.
Summer signing Thiago Alcantara is still suffering from the effects of the knee injury he sustained against Everton on October 17, although there is hope the playmaker may be fit enough to feature against Leicester.
However, the same cannot be said of fellow midfielder Alex Oxlade-Chamberlain, who injured his knee in pre-season training at the end of August and is still yet to resume training.