Lindenberg said winds reached speeds of more than 60 mph.
"It's a warning telling people to take shelter," he said.
Rader said an off-duty sheriff's deputy working security for the boat company helped rescue people after the accident.
Dive teams from a number of law enforcement agencies were assisting in the effort, but the sheriff said the divers ended their search for the night.
The National Transportation Safety Board said on Twitter that investigators will arrive on the scene Friday morning.
Suzanne Smagala with Ripley Entertainment, which owns Ride the Ducks in Branson, said the company was assisting authorities with the rescue effort. Smagala added this was the Branson tour's first accident in more than 40 years of operation.
Branson is about 200 miles (320 kilometres) southeast of Kansas City and is a popular vacation spot for families and other tourists looking for entertainment ranging from theme parks to live music.
Duck boats, known for their ability to travel on land and in water, have been involved in other deadly incidents in the past. They include one in 2015 in Seattle in which five college students were killed when a boat collided with a bus, and one in 1999 that left 13 people dead after the boat sank near Hot Springs, Arkansas.
Safety advocates have sought improvements to the boats since the Arkansas incident.
Critics argued that part of the problem is numerous agencies regulate the boats with varying safety requirements.
Duck boats were originally used by the US military in World War II to transport troops and supplies, and later were modified for use as sightseeing vehicles.
- AP