SAN JUAN, P.R. — For an overburdened pediatrician trying to care for a child who was in pain, needed hip surgery, and was displaced from his home in the wake of Hurricane Maria, it seemed a godsend — a modern military hospital ship sent from its berth in Virginia to help with medical care in Puerto Rico.

But after days calling phone numbers that did not work and trying to navigate the admissions process for the ship, the 894-foot U.S.N.S. Comfort, Dr. Jorge Gabriel Rosado finally gave up. The boy is still awaiting surgery, which had been scheduled for the day before the storm hit more than two months ago.

“It was rough because there were a lot of people that could have taken advantage of all the resources the Comfort had,” Dr. Rosado said. “But there were so many steps to it. Most physicians on the island, even us, decided it was too many steps.”

The Comfort’s mission has ended, but it leaves behind questions about whether it was adequately used during a time of desperate medical need. The ship was prepared to support 250 hospital beds, but over its 53-day deployment, which included travel to and from the island, it admitted an average of only six patients a day, or 290 in total. An additional 1,625 people were treated aboard the ship as outpatients, all at no cost.