Homa Bay County Commissioner Moses Lilan has put on notice fishermen who have "marked boundaries" in Lake Victoria, saying the practice is against maritime law.
Fishermen were causing conflict by marking territories where they operate and keeping others out, Mr Lilan said.
In the latest incident, a 31-year-old fisherman, identified as Michael Juma, who was with four other men, died when his group, from Lela beach, was accused of fishing in an area reserved for another group from Ndhuru beach.
He drowned after their boat collided with another vessel used by Beach Management Unit (BMU) officials to patrol the lake.
His colleagues reported that Juma was unable to swim because he was hit in the head and became unconscious.
His body was found on Sunday morning amid rising tension in the lake as fishermen accused each other of rights violations.
But Mr Lilan said investigations had revealed that the fisherman could have died in a conflict over illegal fishing methods.
Rogue fishermen in the lake are known to use fishing methods that the Kenya Maritime Authority and the Kenya Fisheries Service do not recommend.
To protect themselves from being exposed, Mr Lilan said, such fishermen have set up boundaries in the water that they do not want others to cross.
He said the groups do not allow other fishermen to get near their boats for fear that they will be reported to authorities.
"Conflict in the lake has nothing to do with what is being speculated as boundary disputes. The conflict is a consequence of illegal activities being conducted by people in the lake," he said.
Similar conflicts have been witnessed on Rusinga Island, where fishermen have marked out areas in the lake as their own.
Mr Lilan said authorities have identified some beaches where illegal fishing activities are taking place.
"We will soon launch a crackdown on the beaches and arrest suspects," he said.
Experts warn that using certain fishing nets can lead to extinction of some fish species as the gear catches all sorts of marine life, including juvenile fish.
Other emerging issues in the lake include stealing fishing nets, he said. Such incidents have been reported in the waters between Homa Bay and Migori counties.
"Other fishermen cut nets belonging to their colleagues to release fish back to the lake. The lake is a national resource that is open for everybody who is doing what the law allows," Mr Lilan said.
As the government plans a crackdown in the lake to protect maritime life, there are concerns that some BMU officials will not give necessary support to the KMA, the Kenya Coast Guard Service and other agencies involved in protecting the lake and other resources in and around it.
Such BMU officials are said to engage in acts of corruption, with Mr Lilan warning that they will be disbanded.
"Instead of informing authorities of the existence of nets that are not recommended, they accept bribes from rogue fishermen to continue operating in the lake," Mr Lilan said.
Meanwhile, he has notified sub-county security committees in areas that border the lake to convene meetings with BMUs in their areas to find a lasting solution for problems fishermen are facing.
