A whistleblower who worked in the Electoral Office of Northern Ireland in the run-up to the election described the registration process as "chaos".
He claimed to the Nolan Show that many people wrongly lost their chance to vote due to failings by the office.
The Electoral Office has said the allegations "are not correct".
A spokesperson said staff worked "tirelessly" and that temporary staff were brought in to deal with an increased number of calls.
The whistleblower, who handled calls from the public prior to the general election on 12 December, is not being named publicly.
He claims the Electoral Office gave members of the public an inaccurate deadline date when it wrote to applicants requesting more information.
He says the office told people that the deadline to submit additional evidence, such as proof of address, was 3 December.
However staff were allegedly aware the deadline was 4 December - which was subsequently extended to 5 December.
"People… had followed all the given steps, done everything correctly," the whistleblower told the Nolan Show.
"Nothing which they had done was wrong... there was no real reason why anything was done on their behalf was done to prevent them voting - it was all in the office."
He claimed there was a massive backlog in dealing with registrations and there wasn't enough staff to handle them.
The application deadline for voter registration was the 26 November.
The whistleblower claims that in the days running up to 3 December, the Electoral Office had not processed many of these applications, so if the applicant was asked for extra evidence, they didn't have time to get it in.
Many applications were being processed on the day of the deadline, leaving no realistic timeframe for people to ensure they could provide the information necessary to vote.
He also claims there was confusion in the office over the precise date and time of the deadline for submitting evidence.
He claims that at one stage in November the phones went down on a Friday - and were out all day.
All calls for queries right across Northern Ireland were being taken through a single mobile phone, an old Nokia, which was being passed around between the staff.
The Chief Electoral Officer Virginia McVea, who has suffered a very recent bereavement, issued a statement to the Nolan Show on Friday morning.
She said: "I will not allow the public to be misled.
"The team at EONI work tirelessly for the people of NI and have done for many years. NI receives expert service from an expert team.
"We, like every electoral team across the UK have to employ temporary staff at election times to answer the thousands more calls we get.
"Our phone system is adequate but BT lines were down in Belfast one day.
"We followed their advice on what to do and were treated as priority urgent customers but we have no way to control external infrastructure failures. The staff are well trained over a number of days and continually supported.
"Very importantly it is our whole team, including me, who answer queries and resolve issues through the election period by phone email and in person.
"We are very well used to dealing with queries as our team is expert. Staff advised the public to get evidence in by 3 December at the start to be sure they would have it in in time.
"In the last few days of the lead up staff told people 4 December and every single piece of evidence to midnight on 4 December was processed.
"I have been able to double-check that. All election timetable dates were on our website and available throughout the election."
"We are duty bound by law to keep processing until the deadline and so it's true sometimes we have to ask for evidence right up to the last hours, even if we think a person could not get information in in time, because that is the right of the public and indeed they will go on the register albeit if too late for voting that time."
The whistleblower, who was a temporary staff member, says he told a manager they would be facing a problem of applicants contacting the Electoral Office with less than 24 hours to get that response in.
He says he was advised to send them a complaint form.
When this situation arose in a call, the whistleblower says he told a member of the public who couldn't get their complaint in on time, and that there was nothing he could do, but advised that they might want to contact their local councillor.
This was overheard by a manager who he claims removed him from the phones and he says he was he was dismissed.
Ms McVea added: "I commit to the public to check all processes during the post- election review to ensure continued improvement.
"These claims made my someone who was in our office for a few weeks about large numbers of people being denied their vote are not correct.
"As soon as I return I will move through all the complaints and allegations and questions; indeed we always review such material after an election in order to improve.
"I talk to parties, their administrative teams, journalists and the Electoral Commission all the time about how we can do better.
"We are determined to provide the best service to the people of NI."
The electoral office added: "All applications received before the deadline were processed in time for every successful applicant to be on the register in time to vote on 12 December election.
"Staff advised the public to get their additional evidence to the Electoral Office by 3 December to ensure it was received in time for the legal determination deadline on 4 December.
"Every single piece of evidence received before midnight on the 4 December was processed.
"All absent vote application forms were processed in accordance with the law."
Stuart Wilks Heeg, an expert in electoral law from Liverpool University said the concern is that if these allegations are true, they could affect the election result.
"It is not an easy process to go through, but either an elector who feels that something went wrong in this election, or a candidate, could lodge an election petition," he said.
"They have to do it within 21 days."