Owen Lippert, the NDI's representative in Bangladesh, said his group had checked more than 22,000 names across the country and interviewed 11,000 people during a survey of voters ahead of an election scheduled for January 21.
"The [NDI] delegation is deeply concerned that the new voters' list runs to over 93 million names, a size that is substantially inconsistent with the 2001 census data," Lippert told a news conference.
"A voters' list containing two-thirds of the population strains credibility."
It is feared that Sunday's blockade could turn violent. At least 40 people have been killed in fighting between rival political groups since Begum Khaleda Zia, leader of the Bangladesh Nationalist Party [BNP], ended her five-year term as prime minister in October.
Iajuddin Ahmed, the Bangladesh president and the head of the interim administration, meanwhile is meeting the leaders of both political camps on Saturday in an attempt to resolve the situation.
The initiative came after an envoy of Kofi Annan, the UN secretary- general, called on all parties to come together.
Craig Jenness, director of the UN Electoral Assistance Division, described the situation as "worrying", saying the differences could only be resolved through dialogue.