Only $23.5 million of the $78.2 million budgeted for the project has been provided so far - even though registration is due to begin on 1 December, said UN spokesman Manoel de Almeida e Silva on Sunday.
There is enough money to start the registration process in the cities but it will not be sufficient for rural areas, he added.
"In fact the funds will only allow the project to run until the middle of February, so the ability to produce a credible voter register in time for the 2004 elections depends on sustained donor support."
The budget for the project has already been slashed from an original estimate of $130 million.
The UN spokesman also said that the first elections to pick delegates for a December national assembly meeting would be held in Badakshan province on Wednesday and Thursday.
Elections for the constitutional meeting are to be held elsewhere at the end of November and early December.
Meanwhile, the UN has renewed its appeal to Afghan regional commanders to cooperate with another of their programmes which seeks to disarm 100,000 factional fighters.
Unlikely that 100,000 militia men
will want to disarm voluntarily
The ambitious Japanese-led plan is to begin in the northern province of Kunduz, bordering Tajikistan, on 24 October.
The $200 million project is expected to take up to two years to disarm and demobilise private militias seen as the main obstacle to extending central rule into the provinces.
But many political analysts are sceptical that any serious disarming will take place.
Test of willingness
Silva said the pilot phase, which aims to disarm 1000 fighters in several regions, would be a test of the willingness of commanders to go along with the scheme.
But the escape of Taliban prisoners into the rural areas is unlikely to increase feelings of security.
Afghan authorities said on Sunday they had so far failed to recapture any of the 41 Taliban captives who made a tunnel escape from the main prison in the southern city of Qandahar.
Taliban commander Mullah Sabir told journalists on Sunday the group paid bribes of 100,000 afghanis ($2000) to the prison authorities for each of the escapees.
Sabir said some had already reached their destinations, but he did not say where these were. They included Mawlavi Abd Allah, the brother of former Taliban defence minister Ubaid Allah, and a commander named Aziz Agha.
41 former Taliban fighters all
escaped from the same tunnel
Qandahar police chief Muhammad Jashim said none of the escapees had been recaptured. He said he could not comment on the bribe claim until the investigation was complete.
But Qandahar governor Yusuf Pashtun said that the prisoners, who had been kept in chains, must have had assistance from guards as they had burrowed out an estimated 15 truckloads of earth to make their 30 metre tunnel.
US soldier injured
A soldier from the US-led forces in Afghanistan was injured in a gunbattle with three opposing fighters on the outskirts of Kabul at the weekend, the US military said on Sunday.
One of the attackers was captured in the Saturday night clash near the Afghan National Army's main training centre on the road leading out of Kabul to the eastern city of Jalalabad, a statement from US spokesman Colonel Rodney Davis said.