The deputies who were transporting the two women to a different facility in SC were saved, local law enforcement officials told ABC News late Tuesday.
The deputies waited on top of the van until rescuers arrived.
Aides say President Donald Trump will visit North Carolina on Wednesday to see the damage from Florence.
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"We are now working with the SCDNR to recover the vehicle", Horry County Sheriff Phillip Thompson says. "It could be assumed that he did", Thompson said Wednesday. 'Just like you, we have questions we want answered'.
The South Carolina State Law Enforcement Division is investigating the incident.
Two women "detainees" chained in the back of a police van died when the vehicle was engulfed by Hurricane Florence floodwaters. The two deputies were rescued, the occupants have not been recovered.
The van was traveling west on Highway 76 into neighboring Marion County when floodwaters overcame the vehicle.
The van was traveling on an area near Little Pee Dee River, when waters surged and pushed the van off the road.
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"They're still under the water", he said. Thompson said he has also begun an internal investigation and put the deputies involved - Joshua Bishop and Stephen Flood - on administrative leave.
Justin Bamberg, a state lawmaker and lawyer who has represented the families of several people injured or killed by law enforcement officers, said Wednesday he's perplexed by the decision to transport anyone in such uncertain weather conditions.
Under South Carolina law, people who have been certified by a physician as posing an imminent risk of harm to themselves by virtue of mental illness and are the subject of an involuntary emergency admission must be transported by law enforcement to whichever designated hospital has agreed to admit them, according to officials with the state's Department of Mental Health. The two deaths will push Florence's toll across three states to almost 40 victims.
After submerging North Carolina with almost one metre of rain, the storm dumped more than 16.5cm of rain in the Northeast, where it caused flash flooding.
Police officials told The Sun News that the deputies tried to help the victims, but couldn't open the van doors because the water was rising too fast.
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But others felt that Maria's tragic legacy still needs to be acknowledged, even long after the anniversary has passed. He further said that "3000 people did not die" following Hurricane Maria.