Motorists were caught in the heavy traffic jam as they scrambled for space in one ferry that is operational.
Police officers were deployed to the channel that serves thousands of residents to avoid a stampede.
Kenya Ferry Services has been on the spot over frequent break down of ferries leading to inconvenience.
In March this year, several people were injured following a stampede at the Likoni channel owing to few ferries in operation.
The stampede occurred after two ferries were withdrawn for maintenance by the Kenya Ferry Services, leaving only two in operation.
Some passengers urged the KFS to intervene while laying claim of alleged bribing of police officers by other passengers to enable them jump the queue.
At another time, thousands of commuters were stranded after three vessels developed mechanical problems.
Only one ferry, the MV Kilindini, was transporting commuters across the channel.
From 6am the lone ferry worked to transport passengers, who scrambled to board the vessel, blocking vehicles.
Kenya Ferry Services management added two more ferries to ease the congestion on the mainland ramp.
The two ferries, the MV Harambee and the MV Likoni, were transporting only commuters because they had faulty prowls, while the MV Kilindini ferried only motorists.
The Likoni channel is used by more than 6,000 vehicles and over 200,000 commuters daily.