Lamu boat operators will not be spared in the crackdown for transport safety that is centred on roads.
County Commissioner Joseph Kanyiri announced on Tuesday that they will arrest all coxswains and passengers who do not follow water transport regulations.
The archipelago has more than 5,000 boat operators.
Speaking to the Nation, Mr Kanyiri asked them all to ensure they are armed with business permits from organisations such as the Kenya Maritime Authority (KMA) and the Kenya Ports Authority (KPA).
Officers are alert, he noted, and asked the transporters to prepare for a massive crackdown on all sea vessels that are not compliant.
Unlike other parts of the country where travel is mainly by road, movement in Lamu is primarily by sea.
As such, Mr Kanyiri said more marine police were sent to the Indian Ocean.
"I want to make it clear to the public that the crackdown on vehicles failing to meet the required traffic rules will also target all boat operators in Lamu," he said.
"We have just a few vehicles so as we try to cooperate with the NTSA [for motorists and passengers to comply with] Michuki rules, we advise boat operators to do the same, failure of which we will arrest and prosecute you."
County Police Commander Muchangi Kioi warned boat operators against overloading and speeding.
Mr Kioi also cautioned those whose vessels don't have safety gear such as life jackets, saying they will be arrested and charged with negligence, and the vessels seized.
"Boat operators should know we are also coming for them. Henceforth, they must all carry their licences. It's also necessary to ensure each vessel is registered with the KMA or KPA. Those arrested will serve as examples to the rest," he said.
However, operators who spoke to the Nation asked the government to spare them as business has been slow following the eight percent Value Added Tax on petroleum products.
"It's unfair for us to be subjected to the stresses of Michuki rules. Let them spare us if they care for our trade or else we will be forced to close our businesses," said Mr Musa Iddi, a boat operator.
The operation by the National Transport and Safety Authority and police, that officially began on Monday, has seen commuters walk to their destinations or opt for taxis and personal cars.
On Monday alone, police in Lamu impounded 31 public transport vehicles, 22 motorcycles and 15 people including drivers and passengers, who were found breaching the rules.