All 143 people aboard a military-chartered plane survived after the aircraft skidded off a runway into a river in Jacksonville, Florida, on Friday night, but three pets weren't as fortunate.

The bodies of a dog and two cats were recovered, the Jacksonville Naval Air Station, where the crash landing occurred, confirmed Sunday. An owner safely removed one animal that traveled in the cabin.

"Those who were involved in this sad tasking performed the recovery in the most dignified way possible with the base veterinarian on site to ensure all protocols were followed," the station posted on Facebook. "The animals will be cremated through a local company. Every possible avenue to rescue these animals was pursued following the incident."

Previous reports indicated at least four pets were checked in the luggage department located in the bottom of the plane that left Guantanamo Bay, Cuba, to northern Florida.

Each was presumed dead, Kaylee LaRocque, a spokeswoman for the U.S. Navy in Jacksonville, confirmed to USA TODAY on Saturday.

Although the Boeing 737 plane is not completely submerged in the St. Johns River, the bottom portion, where the pets were positioned, is under water.

“There’s water in the cargo hold," LaRocque said. “We are so sad about this situation, that there are animals that unfortunately passed away."

Authorities have left the plane untouched as the National Transportation Safety Board conducts an investigation of the crash landing, meaning passengers' possessions, including pets, are still on the plane.

Capt. Michael Connor, commanding officer for the Naval Air Station Jacksonville, said the status of the pets became the "second priority" for initial responders after it was determined all passengers were safe.

He said they looked in the cargo bay and did not hear any animal noises or see any crates — a suggestion they were under water.

"So at that point, as well as for their own safety and not knowing if the aircraft could potentially sink and risk their lives, they backed out," he said at a Saturday news conference.

He said he later in the night had first responders do a second assessment in search of pets, but again they did not see any pet carriers above the water.

"Obviously, we do not have confirmation, but we are continuing to do what we can to positively determine the status of the pets," he said, adding that he has spoken to some of the pet owners. "It's a very, obviously, rough situation. My sympathy and my heart really goes out to those families."

LaRocque said earlier Saturday that the pets include dogs and cats. The flight's manifest recorded a total of four pets on board, but she said it's possible more could have been boarded.

"Unfortunately, they have not been retrieved yet due to safety issues with the aircraft, the Naval Air Station Jacksonville, tweeted early Saturday morning. "Our hearts and prayers go out to those pet owners during this terrible incident."

The plane skidded off the runway at around 9:40 a.m. Cheryl Bormann, prominent defense attorney who was aboard the plane, described a chaotic landing in which the pilot appeared to lose control of the aircraft before it smashed into the water and screeched to a halt.

LaRocque said that once the plane is removed from the river, authorities will then retrieve the pets and everyone's luggage.

Authorities haven't said what caused the plane to overshoot the runway. Naval Air Station Jacksonville is a military airport about eight miles south of downtown.