At least two people were killed during a protest to oppose new high fuel prices in the country.
The deaths happened in Gachie, Kiambu County and Nakuru Town, police said.
Several others were injured in the chaos. Witnesses claimed the Kiambu victim was shot and killed.
The one of Nakuru was hit by a speeding vehicle in running battles.
Police said the toll could rise to four after two others were shot and seriously wounded in Gachie.
The police opened fire on a group of protesters who had blocked the road and were harassing other users.
Property of unknown value was destroyed in the chaos. Others were looted in Naivasha and Ruiru, police said.
Anti-riot police were dispatched later in the afternoon to battle with the protesters who had blocked roads.
Thousands of Kenyan commuters were stranded and businesses paralysed as public transport operators went on a nationwide strike to protest against recent increases in the cost fuel.
Key roads in the capital Nairobi remained largely empty, forcing some commuters to walk to work, with other parts of the country also affected by the transport crisis. Businesses in parts of Nairobi remained shut and schools asked students to stay at home.
Protesters have been barricading roads and lighting fires on the roads as the protests continue.
The strike comes days after the authorities raised petroleum prices to record levels, with costs increasing by more than 20%.
Kenya, like many other African countries, relies heavily on fuel imports from the Gulf, a supply route disrupted by the US-Israel conflict with Iran that began on 28 February. Even though a ceasefire has been declared, fuel prices have remained high as the Strait of Hormuz, where a fifth of the world’s oil passes through, is still blocked.
In parts of Nairobi and elsewhere across the country, police clashed with protesters, using tear gas to disperse them. This came amid reports of demonstrators stopping and harassing some motorists.
Ahead of the strike, the police assured Kenyans that security measures would be in place and warned against any disruptive conduct.
The association representing transport operators had earlier urged all vehicle users, including private motorists, public transport buses locally known as matatus and truckers, to stay off the roads as part of a coordinated shutdown.
“This action is not only for transport operators, but for every Kenyan citizen,” the Transport Sector Alliance (TSA) said in a statement.
The alliance accused the government of not doing enough to shield Kenyans from the rising fuel prices, amid a broader high cost-of-living crisis.
It has called for the reversal of the price increases announced last week, and for fuel prices to be reduced by about 35%.
The Energy and Petroleum Regulatory Authority (Epra) on Thursday raised prices to a high of Sh242 a litre for diesel and petrol to Sh214.
Treasury Cabinet Secretary John Mbadi said the strike is completely uncalled for.
“Why are we trying to solve a global problem using domestic means? We have not caused US-Iran war.
“Matatu strike uncalled for. Fuel prices would be higher without government interventions. This is not a time to make emotional decisions,” he said.
The high cost of fuel is being blamed for increases in the price of food and other basic goods and services, with public service vehicles already raising commuter fares.
Last month, the government cut VAT on fuel from 16% to 8% until July but there have been calls for it to do more.
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