In her letter to Acting Labor Secretary Edward Hugler, Warren said she noticed on Tuesday that the site (www.dol.gov/wellsfargo) was gone and contained the words "Page Not Found."
Labor Department spokesman Steve Barr told Reuters the site was removed on January 9, but did not comment further on the reasons why it was taken down.
Former Labor Department Secretary Thomas Perez created the special website last September, shortly after Wells Fargo was ordered to pay $190 million in fines and customer restitution after its high-pressure sales environment led to the opening of as many as two million accounts that customers may not have authorized.
Some of the bank's employees filed whistleblower complaints with the Labor Department's Occupational Safety and Health Administration, saying they had been fired for reporting the "gaming" of sales quotas by Wells Fargo, while others complained that they were forced to work late.
"Taking down this website enables Wells Fargo to escape full responsibility for its fraudulent actions and the department to shirk its outstanding obligations to American workers," wrote Warren, who is a member of the Senate Committee on Health, Education, Labor and Pensions, which oversees the Labor Department.
When he launched the site, Perez pledged to Warren he would conduct a top-to-bottom review of all the Wells Fargo complaints the department had received to see how they were handled.
The website also offered assistance on issues including proper pay for employees and workplace discrimination.
Reuters has reported on issues with some of the whistleblower cases, including one involving a former Wells Fargo employee who waited nearly five years to be interviewed after telling OSHA she was fired for reporting the gaming.
On Friday, Warren also asked for an update on the Labor Department's review.
The findings have not been made public, but a person familiar with the review said that OSHA's San Francisco office, which handled the bulk of the Wells Fargo complaints, faced a particularly high caseload-to-staff ratio.
The review also found that OSHA does not have an effective case management system to track what is going on in the field, the person added.
Labor spokesman Barr declined to comment on that part of the letter, saying he cannot discuss ongoing investigations.
Warren's concerns could resurface on Feb. 7, when fast-food executive Andrew Puzder is expected to appear for his confirmation hearing to become the next labor secretary.
Puzder is already facing a backlash by some of his own workers at CKE Restaurants, who allege they are victims of wage theft.
(Reporting by Sarah N. Lynch; editing by Leslie Adler, G Crosse and Chizu Nomiyama)
By Sarah N. Lynch