Officials at the Naval Air Station Jacksonville, where the Boeing 737 plane landed in the St. Johns River, posted early Saturday that it had not been able to retrieve any of the pets from the cargo of the plane "due to safety issues with the aircraft."
First responders checked the cargo hold after the accident, which occurred at around 9:49 p.m. Friday as the jet coming from Guantanamo Bay went off the runway, struck a seawall and went into the river.
They did not hear any animal noises or see any crates in the cargo hold at the time, but they pulled out for fear the aircraft would sink, base commanding officer Capt. Mike Connor said.
The first priority was human life and getting people off the aircraft. But later in the evening first responders went back specifically to look for pet carriers in the plane’s cargo hold, Connor said.
"They could look in from the cargo bay door. We asked them to specifically look for pet carriers, and they could not see any pet carriers that were above the water," Connor said.
It was unclear how many pets were aboard when the plane skidded into shallow water Friday night. A source told NBC affiliate WTLV reported that one dog and two cats remained inside the plane as of early Saturday afternoon.
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Kaylee LaRocque, public affairs officer at the Naval Air Station, told NBC News that according to the jet's manifest there were four pets inside the aircraft.
After the landing in the river, about 21 people were taken to area hospitals, but were in good condition, a fire official said Friday night. National Transportation Safety Board Vice Chairman Bruce Landsberg said Saturday there were a few minor injuries.
The NTSB said Saturday it had a team of 16 investigators on the scene to determine why the Miami Air International Boeing 737-800 ended up in the river.
Landsberg said the aircraft was built in 2001 and had no history of any prior incidents.
He said the plane's flight data recorder has been recovered and is undamaged, but the cockpit voice recorder is in the tail of the plane and was underwater and had not been recovered yet.
Miami Air International Flight 293 “overran the runway” at the far end on the right side, struck a low seawall made of loose stones and rocks and ended up in shallow waters of the river, Landsberg said.
The pavement on the runway, which is about 9,000 feet long and 200 feet wide, is not grooved, which allows water to run off faster in heavy rain, he said.
"We don’t know if that is a factor yet at this time," he said.
There were some reports of heavy rain but “we haven’t ascertained yet exactly what the weather was at the time of landing, Landsberg said, noting the NTSB investigation has just begun.
Connor said that when he arrived on scene after the accident, the rain showers had stopped and there were no active storms.
"We’ve got some challenges here because the aircraft, the bottom half of the fuselage is covered with water, so we aren’t able to get to all the things that we need to get to," Landsberg said.
Asked whether the plane ever touched down or missed the runway completely, Landsberg said that was not known, but there are skid marks off the end of the runway.
"We could see the track of the nose gear and the main gear off the end of the runway and off to the right side, between where the pavement stopped and when the aircraft impacted the seawall," he said.
Nicole Acevedo is a reporter for NBC News Digital. She reports, writes and produces stories for NBC Latino and NBCNews.com.