Adding to their frustration with the taxes, a number of the utilities have not been reimbursed by FEMA for sending their workers and equipment to Puerto Rico in the first place. That will only take place once a careful review of the invoices is concluded, officials said. Mr. Caetano said that about $940 million of $1.8 billion invoiced for the electrical work has been reimbursed so far.

How storms, missteps and an ailing grid left Puerto Rico in the dark

Some analysts with long experience in the substantial economic, legal and cultural differences between Puerto Rico and the mainland said the tax laws on the island should not be taken as an affront, and that negotiations may yield positive results.

The 15-year recession in Puerto Rico has left municipalities eager to collect taxes, said Tómas J. Torres, executive director of the Institute for Competitiveness and Sustainable Economy, a nonprofit in San Juan. He said that linemen from the mainland making much more than their Prepa counterparts could not help but produce an impression that the utilities could easily pay the tax — whether they made profits in Puerto Rico or not.

“They should not be mad,” Mr. Torres said. “This is an issue of communication and understanding Puerto Rican law more than anything else.” He added, “It’s a matter of sitting down at the table and sorting out any argument that they have.”

Omar J. Marrero Díaz, Puerto Rico’s chief recovery officer, appointed by Gov. Ricardo Rosselló, said he knew of “seven or eight” municipalities that had sent tax bills. Part of the reason they are desperate for money, he said, is that like the utilities themselves, they are still waiting for FEMA to disburse funds — in this case, most of the $3.7 billion allocated for disaster relief.

“We have been trying to serve as a mediator between the companies and the municipalities,” said Mr. Marrero, adding that some mayors have indicated a willingness to compromise or waive the taxes. “That’s the way we feel, even though we have been complying with the overly bureaucratic process” at FEMA, he said.

On the time frame for payments, Mr. Caetano said, “We trust but verify. The speed of disbursement is driven in a large part by the quickness by which we receive accurate and required paperwork from our partners.”