"There are centers that existed in the electoral commission's map that are not open and others that are open when they should not be," said opposition candidate Martin Fayulu, who came second in the last election.
"There have been many problems with the power sources of the machines and delays in the delivery of kits, solar panels, cables," he told Reuters on Thursday, accusing the CENI of "organizing electoral chaos to prepare for fraud."
Over 50 million DRC voters are meant to be registered by March 17, but the CENI election commission said an unspecified number of centers in the first registration zone of 10 provinces that includes the capital Kinshasa had missed an interim deadline - that had already been extended by 25 days.
A further 24 centers in Kinshasa province and an unspecified number of centers in Mai Ndombe province had not opened because of security issues, it said.
"They will be granted a catch-up period," CENI rapporteur Patricia Nseya said in a statement that cited operational difficulties without giving further detail.
An internal CENI document seen by Reuters showed that 779 of the first zone's 9,200 registration centers were closed or not operational as of Feb. 1 and only 52% of forecast voters were registered.
Alleged irregularities, including faulty voting machines and delays opening some polling stations, marred the last presidential vote in 2018 which Fayulu still claims he won by a landslide.
He and fellow candidate Moise Katumbi told Reuters they believed the CENI was prioritising registering voters in areas loyal to President Felix Tshisekedi like his home region of Kasai.
"There are more enrolment machines in Kasai than in other more populated areas like Katanga," said Katumbi, a businessman and former governor of wealthy Katanga province, who announced his candidacy in December.
Three Congolese and international electoral experts, speaking to Reuters on condition of anonymity, also said they had noted a discrepancy between the number of registration kits available in pro-Tshisekedi and opposition areas.
The CENI last week said it would respond to a Reuters request for comment on the allegations, but it had not replied as of Monday.
On Friday, the influential electoral observation mission of the Catholic and Protestant churches, said it hoped "the electoral commission could find a calm moment to clarify the situation of the registration centers that our observers have not been able to find on the ground."
The mission has reported more than 200 incidents in the last two weeks, such as delays in the arrival of equipment and malfunctions that prevented the registration of voters.
