Three family members drowned at the Likoni Ferry crossing after their vehicle plunged into the deep waters.
One body was retrieved from the waters by divers after an hour's search.
Search for the remaining two was called off as night fell and due to lack of diving facilities.
A team from the Kenya Navy at Mtongwe arrived at the scene of last evening's tragedy to help in retrieving the bodies. The victims' vehicle, a Toyota Probox, is said to have plunged into the deep sea as it reversed while disembarking from MV Likoni.
A Kenya Ports Authority employee, Joel Masindano, was among those who drowned. He was heading home from work. "He had left office for home and the car that plunged was his," said his co-worker Veronica Mutua.
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The incident brought operations at the ferry to a standstill as the divers struggled to retrieve the body.
Confirming the incident, Likoni OCPD Wilies Simba said one body had been retrieved and the search for the other two missing bodies was ongoing.
He said the driver of the ill-fated vehicle was coming from the main land to the island.
"At around 5pm the driver of the Probox engaged the reverse gear instead of the forward gear and he plunged into the ocean," said Mr Simba.
He said concerted efforts were being made to recover the other two missing bodies.
Moses Sila and Mohamed Mnyekombo said there was one body lying 10m from the vehicle in the 60m-deep waters.
Mr Sila said they found the vehicle upside down and three windows open — a sign that the victims had struggled to get out of the vehicle.
"We only found the driver's body about 10m away from the vehicle that was upside down. However, we could not continue with the search due to darkness and lack of lighting equipment," said Sila.
According to Sila, there are no divers and equipment at KFS to immediately save drowning victims.
