Sudan's opposition has long complained the requirements for standing for the presidency were too tough in Africa's largest country, devastated by decades of civil war. Candidates must gather 15,000 supporting signatures from 18 of 25 states.
The opposition says the commission's stringent rules are to skew the vote in favour of Bashir's party, which has ruled since taking power in a bloodless coup in 1989.
Many parties want to field multiple candidates to split the vote and prevent Bashir getting the 50 per cent plus one vote he needs to win, forcing a second round where they would support the opposing candidate.
'Discrimination against women'
The only female candidate, Fatima Abdel Mahmood, leader of the Sudanese Socialist Democratic Union, said the ruling was a conspiracy against women and the party would appeal to the courts.
"This is a form of discrimination," she told Reuters news agency.
Her deputy Abdullilah Mahmoud said the NEC rejected them as they had not stamped their papers at state level, despite being told by the NEC leadership that the central office in Khartoum could do that when they handed their papers in a day ahead of the January 27 deadline.
"We even collected our signatures twice because the first time they said it had to be done on their papers," he said.
"When we handed in our papers again they said they were accepted. This is their error not ours."
Independent candidate Abdallahi Ali Ibrahim said he had expected to be rejected as he had collected 16,000 signatures from only 15 states, but had submitted his candidacy anyway to highlight the problems with the system.
"We have a percentage of illiteracy of 70 per cent in this country but they ask for 15,000 signatures," he told Reuters.
He said he doubted the elections would be free or fair "not just because the government is dictatorial but because the other dancer in this tango is a bad dancer."
Ibrahim was referring to what he called the weak opposition who have, despite complaints, accepted all the electoral irregularities and continued their campaigns.
The election system will require about 1,000 different ballot papers for at least six different votes and has been called one of the most complex in the world.