NEW YORK — Amazon on Tuesday suspended more than two dozen employees at a large warehouse on Staten Island who had refused to work their shift the previous evening, hours after a cardboard compactor at the site had caught fire.

The paid suspensions will last while an investigation takes place, according to a company email to the employees that was shared by the Amazon Labor Union, which won a vote to represent workers at the warehouse in April.

Dozens of employees had gathered in a break room Monday night, raising concerns about fire safety and refusing to work. Some worried that the air at the warehouse might not be safe to breathe because of smoke or fumes from the fire.

The company confirmed the suspensions, saying that it respected employees’ rights to protest working conditions but that occupying work spaces was inappropriate.

Under federal labor law, employees have a right to engage in so-called concerted activity for “mutual aid or protection,” such as protesting a dangerous work environment. The union said it intended to file an unfair-labor-practice charge in response to the suspensions.

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Night-shift workers complained Monday that supervisors had told them that they would have to work despite the fire earlier in the day, even though workers who had been on the job during the fire were sent home with pay.

“Workers want to go home,” Derrick Palmer, an employee at the warehouse who is vice president of the Amazon Labor Union, said in an interview Monday night. “They sent the day shift home, but they’re making the night shift stay.” (Palmer works the day shift.)

In an initial statement Monday night, Amazon said it had asked night employees to report to their shifts after the fire department certified that the building was safe. “While the vast majority of employees reported to their workstations, a small group refused to return to work and remained in the building without permission,” the statement said.

Connor Spence, another employee at the warehouse who is the union’s treasurer, said some employees had eventually returned to their workstations, while others had gone to the main office at the site to continue their protest.

Amazon has challenged the results of the union election on Staten Island, and the two sides have yet to begin bargaining over a contract. Workers at another Amazon warehouse, near Albany, New York, will begin to vote next week on whether they want to join the Amazon Labor Union as well.