On Tuesday, however, a televised army statement read: "The Egyptian Armed Forces can not ignore that Anan has committed legal violations that constitute a serious breach of army regulations".
The statement also accused Sami Anan of forging paperwork that showed his military service had ended, which the Armed Forces denies.
A presidential candidate in 2012, the 45-year-old Ali said he had been forced to pull out of this year's election to be held on March 26-28.
Anan had announced his intention to enter the race, two hours after current President Abdel Fattah Sisi declared his plan to seek a second term.
Egyptian presidential hopeful and rights lawyer Khaled Ali says he is withdrawing from the race.
According to the Presidential elections law and the Egyptian constitution, presidential Candidates must receive endorsements from a minimum of 20 MPs, or 25,000 citizens from at least 15 governorates, with at least 1,000 endorsements from each governorate.
Anan's arrest came a week after he announced his presidential aspirations on his official Facebook page, promising reform.
Egyptian president to brief AU leaders on continent's peace, security issues
The Commission will continue to receive candidacy requests until January 29.
Since the ouster of former Muslim Brotherhood-affiliated President Mohamed Morsi, Egypt has been witnessing growing waves of extremism that harmed society, such as the terrorist attack that hit Al-Rawdah Mosque and left more than 302 Friday prayer congregates dead in late November. In his video announcing his candidacy, Annan spoke of deteriorating living standards and what he called the "erosion" of the state's capabilities, and he blamed it on the policy of increasingly involving the military in the economy and politics.
Ahead of the vote, the overwhelmingly pro-el-Sissi media have been building a personality cult portraying him as the only man qualified to lead, while denouncing each potential challenger.
"Now we'll have to wait and see who will come up, probably somebody who does not have that much support on the ground and does not have any support in the military establishment", Ashour said.
Ali said he had aborted his campaign because of overwhelming obstacles that had prevented him from even getting on the ballot, and accused the elections committee of "violations". Among them was a former prime minister, Ahmed Shafiq, who aides said had been pressured to quit under threat of prosecution on corruption charges, and Anwar Sadat, a nephew of the former president.
Ali also cited a case filed against him, where he was sentenced in September in absentia to three months in jail on accusations of "offending public decency", a ruling he appealed.
The boxes contained "recommendations" from voters who want el-Sissi to run for a second, four-year term.