Citing financial constraints, Harvard Medical School will cut 31 custodial contract jobs, a move that has prompted criticism from the labor union that represents the workers and the circulation of an online petition opposing the decision.

The cuts, which will take effect on August 17, stem from the cancellation of the Medical School’s approximately six-and-a-half-year-old contract with American Cleaning Company, Inc., a Brighton-based subcontractor that services the Medical School. Harvard notified American Cleaning Company of its plans last month.

About 90 people currently hold custodial jobs at the Medical School, according to Richard M. Shea, the Medical School’s associate dean for campus planning and facilities. The approximately 60 remaining workers, who are employed by the Medical School rather than an outside subcontractor, will keep their jobs when the cuts take effect next month.

As reasoning behind the cuts, Shea cited the need to address the Medical School’s “high operating deficit,” which he said is projected to total about $40 million for the 2013 fiscal year. He estimated that the 31 cut jobs could save the Medical School up to $1 million.

“It’s never easy to do anything like this, because they’re people—we care about that,” Shea said, explaining that it was important to try to keep the jobs of the custodians that the Medical School hires directly.

Still, Service Employees International Union Local 615, the labor union that represents both the custodial workers hired directly by the Medical School and those contracted through American Cleaning Company, has spoken out against the decision.

Following Harvard’s notification, the union began soliciting signatures in an online petition expressing opposition to the cuts, according to Wayne M. Langley, the director of higher education for SEIU Local 615. The petition, which Langley said is also being distributed in paper form, says that the cuts “would be effectively trimming the budget on the backs of [the Medical School’s] lowest-paid workers.”

Barbara Bastardo, a custodial worker at the Medical School contracted through American Cleaning Company, said she reacted to the news that she would lose her job with incredulity.

“How could it be that a University as prestigious and as rich as Harvard doesn’t have enough money to pay the lowest-paid workers within the institution?” Bastardo said in Spanish through a translator.

However, Gina Vild, associate dean for communications and external relations at the Medical School, wrote in an email that the claim that the custodial workers are the Medical School’s lowest-paid workers is incorrect.

In a phone interview Monday, Langley suggested that the cuts demonstrate an “anti-worker bias,” arguing that Harvard should cut executives’ salaries rather than the workers’ jobs. He added that he considers the differentiation between the workers hired by the Medical School and contracted through American Cleaning Company an “artificial distinction,” noting that both groups of workers are paid the same wages, which Vild confirmed.

Shea said the Medical School is evaluating its operations across the board to address the operating deficit. With fewer custodial workers, Shea said there may be changes to cleaning standards, such as the frequency with which the trash is emptied. Adding that the details are still being worked out, Vild wrote that the current Medical School custodians “are not being asked to take on additional duties.”

The cuts are not the first sign of financial worries at the Medical School this year. The Medical School’s operating deficit for the 2012 fiscal year was $28.8 million, according to the Boston Globe. And in April, when the Medical School announced the closure of its New England Primate Research Center—which became the source of controversy after the death of several primates—it also cited financial constraints.

—Staff writer Madeline R. Conway can be reached at mconway@college.harvard.edu. Follow her on Twitter @MadelineRConway.