Due to security concerns, officials refused to discuss specific changes in deployment timelines or the units involved, but sketched out how they could impact overseas deployments into 2018.
Defense Secretary James Mattis spoke about the challenge publicly for the first time Tuesday, testifying before the Senate Armed Services Committee that the military will stay in Puerto Rico as long as needed: "We are ready to go even to the point that it's going to impact the deployments, perhaps, of some of these troops overseas next year because we've interrupted their preparation."
The impact is already being felt on troop deployments to Afghanistan. Planners are considering several solutions including delays for troops scheduled to deploy, either as part of the additional 3,500 troops being sent, or to replace existing forces.
Forces scheduled to come home may not be able to leave Afghanistan until their replacements arrive, and some departing troops may have to leave equipment behind until aircraft can be sent to pick it up.
It's also the case that troops being sent to the country may have to travel to Europe on short-haul military flights and then switch to other aircraft to keep airlift cargo planes free to keep moving hurricane supplies.
One official said the delays will impact US military operations in Afghanistan and the desired plan is not to delay troops more than two weeks.
The Pentagon confirmed in a press conference on Thursday that some delays would occur due to constraints on resources.
"There are going to be delays. I think the delays are relatively minor," Lt. Gen. Kenneth McKenzie, the director of the Joint Staff, told reporters at the Pentagon Thursday.
"There's a finite number of transport aircraft that US Transportation Command has. We're moving things to Puerto Rico, we're doing a variety of things to help down there," he added, saying: "Given the fact that we have a finite number of transport aircraft, that will inevitably slow movement to other theaters and the slight delay in the flow of forces to Afghanistan (is) just sort of a natural component of that."
But McKenzie said the delays were acceptable due to the urgent need to provide aid to Puerto Rico.
"The secretary said we're all in to help Puerto Rico and there are just going to be downstream effects when you make those decisions," he said. "But American citizens are involved in Puerto Rico, and that's a very high priority for this department. So we're probably going to accept some downstream delay as a result of that."
There are also impacts at sea. The amphibious assault ship USS Wasp has been in the Caribbean since Hurricane Irma hit and is now ferrying supplies into Puerto Rico. This week, 13 additional helicopters were put aboard to increase the number of relief flights into the hardest hit areas of Puerto Rico, according to a Navy official.
Originally, the Wasp was scheduled to deploy to Sasebo, Japan, when it left Norfolk on August 30, but it never made it past the Caribbean because it was needed for hurricane relief. It was due to replace another amphibious assault ship in Japan, the USS Bonhomme Richard, which had been scheduled to return to the US for long-term maintenance.
The Wasp was also due to accommodate Marine Corps F-35s jets and become a key platform in the region to demonstrate advanced US airpower amid rising tensions with North Korea. Several officials say it's now not clear when this will happen.
"Certainly, that's going to slow the deployment of that ship to the Pacific, and it's going to have a cascading effect. So it could be very likely that when the secretary talked about things that might affect in the next year, that's what he had in mind," McKenzie said Thursday.
All of this comes as several defense officials confirmed to CNN that military planners are reviewing whether it may be possible to hold major military exercises in the western Pacific with three aircraft carriers, as well as forces from South Korea and Japan. They all declined to discuss the specifics of future deployments, but it's possible the administration could send two or more carriers to the western Pacific as part of an effort to further demonstrate American military power to allies in the region and to North Korea.
The carrier USS Ronald Reagan is currently in Hong Kong and will continue with its long-scheduled deployment through the region and could be sent back toward the Korean Peninsula. The USS Theodore Roosevelt is expected to deploy by the end of the year from the US, and will also transit through the western Pacific.
The USS Nimitz will be sent back to the US across the Pacific from its current deployment in the Middle East. What is unclear at this point is if the carriers will converge at some point in the Pacific. If the Roosevelt does not immediately replace Nimitz in the Middle East, that would leave the US without a carrier in the region, something military planners would be loath to allow.