"It is absurd that in Brooklyn, New York -- where I was born, actually -- tens of thousands of people as I understand it, have been purged from the voting rolls," Sanders said during an evening campaign rally at Penn State University.
In an email to CNN, Sanders spokesman Karthik Ganapathy called the state's handling of the primary a "shameful demonstration."
"From long lines and dramatic understaffing to longtime voters being forced to cast affidavit ballots and thousands of registered New Yorkers being dropped from the rolls, what's happening today is a disgrace," he said.
Election Justice USA, a voter rights organization, told CNN it will go to Federal District Court in Brooklyn on Wednesday morning as part of an effort to have provisional ballots from voters disenfranchised by the Board of Elections counted before the primary results are certified.
Earlier in the day, a federal judge denied a temporary restraining order filed by the group that would have opened the polls to New York Democrats claiming they were unlawfully listed as Republican or unaffiliated.
A little before the polls here closed at 9 p.m., the polling site coordinator at Brooklyn Borough Hall estimated that about 10% of those who showed up to vote on Tuesday were previously removed by the board of elections. More than 2,800 people had voted at the location.
New York Mayor Bill de Blasio, a Hillary Clinton supporter, called for major reforms to the Board of Elections as a series of snafus continued to bubble up, including reports of the errant "purge" in Brooklyn.
"It has been reported to us from voters and voting rights monitors that the voting lists in Brooklyn contain numerous errors, including the purging of entire buildings and blocks of voters from the voting lists," de Blasio said in a statement Tuesday calling on the board to "reverse that purge."
"The perception that numerous voters may have been disenfranchised undermines the integrity of the entire electoral process and must be fixed," he said.
Speaking to CNN on Tuesday night, Board of Elections Executive Director Michael Ryan pushed back against the growing criticism, saying, "We're not finding that there were issues throughout the city that are any different than what we experience in other elections."
Of the 126,000 Democratic voters taken off from the rolls in Brooklyn, Ryan said 12,000 had moved out of borough, while 44,000 more had been placed in an inactive file after mailings to their homes bounced back. An additional 70,000 were already inactive and, having failed to vote in two successive federal elections or respond to cancel notices, were removed.
"Since the eyes and ears of the world are on New York, issues that are relatively routine for any election are receiving greater scrutiny," he added.
In pledging to audit the board, the office of New York City Comptroller Scott Stringer issued a much stricter verdict.
"The people of New York City have lost confidence that the Board of Elections can effectively administer elections and we intend to find out why the BOE is so consistently disorganized, chaotic and inefficient," he said.
The Clinton campaign had no immediate comment when asked by CNN.
New York Attorney General Eric Schneiderman's voter complaint hotline had "received more than 700 complaints from voters across (New York state)" before 4 p.m., Schneiderman spokesman Nick Benson tweeted. The same office, he added, had heard only around 150 on the day of the 2012 general election.