The administrative court suspended the election after it emerged the date had been wrongly set by an independent electoral commission, and not by the military council who rule the country.
Adding to the confusion, the suspension itself is now in doubt after separate officials questioned the court's authority to suspend the vote.
Despite the suspension, legal experts have said they are confident the election will go ahead as planned and candidates have continued to campaign and prepare for the first televised debate on Thursday night.
Egypt's ill-defined mix of overlapping authorities, which include the ruling generals, the old constitution and recent edicts mean it is nonsense to think that this is a fully functioning legal system, lawyer Michael Wahid Hanna told the New York Times.
Last month, the country's former Prime Minister under Hosni Mubarak was barred from taking part in the presidential race.
Acting under the newly ratified 'Corrupting of Political Life; Law, which bans certain figures who served under the ex-president, the Supreme Presidential Electoral Commission made Ahmed Shafiq the latest person to be expelled from the vote.
Three other leading candidates were also banned from the race in April: Salafist Hazem Abu Ismail, because his mother had an American passport; the Muslim Brotherhood's Khairat Al-Shater, due to a recent prison sentence, and Mubarak intelligence chief and vice president Omar Suleiman.