Ayman Nur, leader of the liberal Ghad (Tomorrow) Party, said on Friday his group was the first to turn up at the headquarters of the Presidential Election Commission when it opened to receive nomination papers in the morning.
But he failed to obtain any assurance that the names would be listed in the order in which candidates submitted their papers or even that they would be in alphabetical order, he said.
In Arabic, Nur would come before Mubarak alphabetically.
"There was a disagreement on that point. The chairman of the commission (judge Mamdouh Marei) said the commission would study the matter," he said by telephone.
Mubarak announced on Thursday he would stand for a fifth six-year term as leader of the Arab world's most populous nation, in the first presidential elections ever with more than one candidate.
The politburo of the ruling National Democratic Party endorsed the president's nomination by consensus later in the day.
Nur is expected to be Mubarak's most prominent opponent; but after decades of authoritarian government and state domination of the domestic media, analysts say he has no chance of winning.
Police had arrested Nur in January and he is on trial on forgery charges which he says are meant to discredit his election campaign.
The next session of the trial will not take place until 25 September, after the elections.
The state news agency MENA said that Usama Shaltut of the little-known Takaful (Solidarity) Party also submitted his nomination papers on Friday.
Some of the big parties, including the leftist Tagammu and the Arab nationalist Nasserite Party, have decided to boycott the elections, on the grounds that the authorities have given insufficient assurances that voting will be free and fair.