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SAN JUAN — Puerto Rico saw a spike in crime over the holidays, as thousands of police officers called out sick in protest of not being paid for countless hours of overtime worked in the aftermath of hurricanes Irma and Maria and in frustration over the island’s lingering economic crisis.

Police stations in over half of Puerto Rico’s 78 municipalities were forced to close in recent days as the increase in absences reached alarming levels.

The situation has grown so dire that Gustavo Gelpí Jr., the federal judge who oversees a reform agreement for the Puerto Rico Police Department, on Saturday ordered the department's high command and the island's Department of Public Security to meet with the U.S. Justice Department to come up with ways to end the "unprecedented massive absenteeism."

He ordered them to submit possible solutions to the court by Friday, warning that because "public safety is a priority," there will be no extension of the deadline.

Gelpí also urged all police officers to return to work.

And on Monday, Puerto Rico's governor, Ricardo Rosselló, issued a statement that he had accepted the resignation of police commissioner Michelle Hernández de Fraley, the first woman to have held the job.

While the governor named an interim commissioner, Lieut. Col. Henry Escalera, from within the department, he said that he would also be looking outside the island for a replacement — as they are doing with the candidate to head the island's beleaguered power authority.

Related: Puerto Rico governor announces task force to examine hurricane-related deaths

Though no reasons were given for the resignation, it comes amid the controversy over officer absenteeism and reports of clashes between Hernández de Fraley and the island's Public Safety Secretary Héctor Pesquera.

The island has seen an increase in reports of murders, robbery and carjackings in the first week of 2018. Official statistics indicate that so far this year, there have been 25 murders, 15 more than reported in the same period of 2017, according to Puerto Rico's Police Department.

Puerto Rico’s police force is the second largest in the U.S., with about 13,600 officers. On average, about 550 to 600 officers call out sick each day across the island. But lately, the number has been in the thousands.

On Jan. 1 alone, the department reported that 3,335 officers called in sick for the day's first shift. The number rose in the second shift to 3,501. It was unclear how many called out for the third and final shift.

With half the island's population still without power, residents are becoming nervous over the lack of law enforcement on the street. Gabriel Calderón, 58, who lives in Loíza, about 17 miles east of San Juan, said he had changed his social life to make sure he is home early everyday.

“I do not like it, but I have to lock myself up in my house and stay like that while this changes,” he said.

Exacerbating the situation, 301 police officers retired at the end of 2017, and the Police Department did not answer a question as to whether the officers will be replaced.

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Puerto Rico’s government, facing a massive debt crisis, says that it is waiting for the Federal Emergency Management Agency (FEMA) to reimburse it for the police overtime pay and that is a slow process.

“Little by little we will pay,” said the Public Safety secretary, Héctor Pesquera, whose department includes the police force and other emergency services.

Pesquera met with leaders of police unions and acknowledged that not only is FEMA an issue, but the way overtime hours are recorded is “bureaucratic and obsolete” and must change. Officers have to fill out time sheets by hand in order to get paid.

Pesquera stated that more temporary staff would be hired to go through the officers’ time sheets to process overtime pay, but he did not commit to a firm date for payment.

Puerto Rico’s governor, Ricardo Rosselló, said all absences will be investigated and if they are not justified the officers will be reprimanded.

The officers’ anger goes beyond unpaid wages, however. The police force has endured the ramifications of a recession that has lasted over a decade. A series of austerity measures taken to deal with the commonwealth's economic crisis have affected government employees, including police officers, who are no longer paid for unused sick days.

Family members eat dinner at dusk with light from a cell phone on Dec. 21, 2017 in San Isidro, Puerto Rico. The community was hard-hit by Hurricane Maria and remains mostly without grid electricity. Mario Tama / Getty Images

Police pensions have also been cut. In the past, officers who worked 30 years would receive 65 to 70 percent of their salary, but that has now dwindled to 30 to 35 percent, according to The Associated Press.

But it's been the delay in paying overtime that has prompted the police sickout.

In the aftermath of Hurricane Maria, many officers showed up for work day after day, despite struggling with dire situations at home. Because of the magnitude of the emergency, many officers worked over 12 hour shifts without a break. Many didn’t have a day off in over two months.

Now they say staying home is the only way they can press the government to pay what they are owed.

In the past few days, police union leaders have warned that officers will continue to call in sick if they are not paid the overtime due to them and their demands for retirement plan changes are not met.

“Months ago, they were warned that this was going to happen," Ismael Rivera, president of the Puerto Rican Police Union, said of the absenteeism. "Now we are saying that this is going to get worse."

Jaime Morales, executive director of one of the police associations, the Organized Police and Security Corporation, says the sickout will persist because hiring temporary staff, as Pesquera mentioned, will take time.

“There will be some administrative changes, and we don’t know how long it will take to execute them,” he said.

Related: Anger grows and hope fades as Puerto Rico's ground zero remains without power

Jorge González Ortiz, an attorney for the American Civil Liberties Union in Puerto Rico, said in a recent interview that the recent police absences absences reflect "mistreatment" on the part of the police department.

“Many of these policemen have almost inhuman shifts," Ortiz said. "They and their families have the same problems as the rest of the population."

Ortiz said that while the ACLU has been critical of the department in the past — the ACLU filed a lawsuit that resulted in the 2013 consent decree between the island's police department and the Justice Department to reform the department and curb abuses — he said that as workers, police "have been mistreated."

Julio Cintrón, an officer who has been with the police force for 22 years, has been out sick because he says post-hurricane stress has aggravated his hypertension and anxiety.

“I'm very upset, very upset, because I thought that today at least I could have had even an extra bit of money in my bank account,” Cintrón said.

A car drives under tilted power line poles in the aftermath of Hurricane Maria in the Punta Santiago beachfront neighborhood in Humacao on Dec. 8, 2017. Ricardo Arduengo / NBC News

He complained that police officers routinely pay for oil changes and tire repairs for patrol cars as well as cleaning supplies for the police station. “Our salary does not match what we do,” he told NBC News.

But Cintrón considers the core issue to be the changes to the pension plan. He described it as asking a brother to hold a portion of one’s salary each month to save for the future, then one day the brother says, “Because I wanted to duplicate your money ... I bet everything and I lost it, and now I don’t have any left," Cintrón said.

“Well, now many agents do not want to work," he said. "They do not know what else to do.”

Additional reporting by NBC News contributor Carmen Sesín.

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