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Captain Michael Connor, the commanding officer of NAS Jacksonville, described the passengers as a mix of military personnel and families, and a few civilians. While some were staying in the area, others planned to fly on to other parts of the country.

‘‘I think it is a miracle,’’ Connor said. ‘‘We could be talking about a different story this evening.’’

Passengers lined up on the plane’s wings before climbing into rescue boats, said the base’s fire chief, Mark Brusoe.

Several pets were on the plane as well, and their status wasn’t immediately clear. A navy statement early Saturday offering ‘‘hearts and prayers’’ to their owners said safety issues prevented rescuers from immediately retrieving the animals.

It wasn’t immediately clear what went wrong. Boeing said in a tweet Friday night that it was investigating: ‘‘We are aware of an incident in Jacksonville, Fla., and are gathering information.’’ The Federal Aviation Administration was referring media inquiries to NAS Jacksonville. The National Transportation Safety Board dispatched a team of 16 investigators to determine what happened.

Connor said he didn’t know what impact the weather had on the flight. ‘‘I was at home when this happened and there were thunderstorms and lightning,’’ he said.

The flight was a regular charter run by Miami Air International, which has many military contracts, including weekly flights between the US base in Cuba and the Jacksonville air station as well as Andrews Air Force Base, Md. The company didn’t immediately respond to messages from The Associated Press.

The same plane had been expected to return to Cuba on Saturday to carry other members of the military, lawyers, and others to Andrews after this week’s military commission hearings of people charged with war crimes. The US still holds 40 men at the detention center in Guantanamo Bay, including five charged with planning and aiding the Sept. 11, 2001, terror attacks.

It wasn’t known how long it would take to remove the plane from the river, but Connor said the landing gear appeared to be resting on the river bed, making it unlikely for the aircraft to float away. He said crews began working to contain any jet fuel leaks almost immediately after securing the passengers’ safety.

The chemical smell of fuel and oil was pungent as journalists took a boat for a closer look. The bottom of the plane was under water, making it difficult to access the cargo hold, and the plane’s nose cone was missing.

‘‘We’re obviously very concerned about the environment and we’re doing everything we can to contain it,’’ Connor said about the fuel. ‘‘Once we were assured that personnel were safe, our next priority effort was to . . . contain any type of fuel.’’

Jacksonville Fire and Rescue tweeted that approximately 90 personnel responded to the scene, and that the department’s special operations team had just trained with marine units for a similar incident earlier Friday.