Kenyans walked to their places of work as others paid exorbitant fares when police began enforcing stringent traffic regulations popularly known as Michuki rules.
Many matatus and buses kept off the roads.
The Transport and Interior ministries had set Monday as the deadline for complying with the rules put in place 15 years ago to restore sanity on roads.
A public service vehicle should be fitted with seat belts, a speed governor and must have a bold continuous yellow line.
Drivers and conductors must be in uniform and their photos displayed in their vehicles.
Nairobians were trekking from their homes from as early as 4am as police impounded vehicles.
Police arrested more than 2,500 offenders, with many vehicles being impounded.
The crisis did not spare Kenya Certificate of Secondary Education examination candidates.
Later in the day, Matatu Transport Vehicles Association Secretary-General Richard Kanoru said members of the organisation would comply with the 2013 Traffic Act and would be back on the road this morning.
"We will follow the rules. Even matatus that have a capacity of 26 passengers and less will have the yellow line. We had to make sure that there would be no harassment," Mr Kanoru told reporters.
Matatu Owners Association chairman Simon Kimutai confirmed the statement, adding that a meeting between the Transport Ministry and PSV stakeholders was held to address concerns raised by the operators.
"We agreed that all vehicles and crews that are back on the road would comply with the Traffic Act. The laws were there, only that they were not being implemented or followed," Mr Kimutai said.
Interior Cabinet Secretary, Fred Matiang'i said the crackdown on vehicles that are not compliant with the rules would continue.
He told matatu operators to keep their vehicles at home if they do not wish to comply.
"The fight to restore order on our roads is on. We had a feeling that PSV operators would go on strike. We will fully support those who are ready to follow the law. These are not new rules," Dr Matiang'i said.
Transport and Infrastructure Minister James Macharia also said the crackdown would go on.
"We may withdraw licences of the vehicles that were not on the road today. Why would we give you a permit you are not prepared to use?," Mr Macharia said at the Railways Station in Nairobi.
The CS added that operators who took advantage of the situation to increase fares would be disciplined.
In parts of Nairobi, commuters paid two or three times the ordinary fare because of the scarcity of vehicles.
Mr Macharia also ordered Kenya Railways to increase the frequency of commuter trains and reduce fare by 10 per cent. There will now be six more trains operating in the city. On Monday morning, 16,000 commuters used the trains. Following the minister's order, commuters will pay between Sh35 and Sh60 per trip.
"To ensure the public continues with the day-to-day activities, Kenya Railways Corporation is directed to increase the number and frequency of trains and reduce fare," the minister's statement said.
During the crackdown, a police officer sustained injuries when her finger was bitten a driver.
Eldoret South police boss Wilson Abduba said the driver and his wife were arrested and the vehicle detained.
Boda bodas and private cars charged a passenger between h250 and Sh700.
The fare from Chuka to Nairobi was Sh1,000, up from Sh500 while one travelling from Nairobi to Chuka paid Sh1,500.
It cost Sh800 from Maua to Chogori, yet ordinarily, one pays ShSh300. Fare from Meru to Nairobi shot to Sh1500.
"It has been a chaotic morning," Mr Kevin Acheda, a resident of Utawala estate in Embakasi said. He works in Kilimani.
He said there were hardly any matatus on the road when he got to his bus stop. Whenever one arrived, boarding it was a battle despite the crews charging Sh200 instead of Sh80.
Mr Kevin Andere, who commutes from Embakasi to the City centre was a little lucky. Most matatus on Jogoo Road from Fedha Estate increased the fare by Sh20.
The situation was the same in other parts of the country, with police vehicles coming to the rescue of stranded KCSE examination candidates in Mombasa, where 28 matatus were impounded. Changamwe OCPD Peter Omanwa said the candidates reached their centres on time. More than 180 drivers and passengers were charged with flouting traffic rules in Mombasa.
Some of the suspects were charged with driving unroadworthy vehicles that had broken glasses, others had no uniforms while others failed to fasten the seat belts.
A majority pleaded guilty to the charges and were fined between Sh10,000 and 50,000.
Passengers who were charged with failing to buckle up were told to pay Sh500 or spend a month in prison.
In Kisumu, at least 23 vehicles and 16 motorcycles were seized at Old Airport on Busia road.
County Police Commander Job Boronjo said the vehicles did not have speed governors, seat belts and the yellow lines. Some drivers and conductors did not have uniform and badges.
In Nakuru and Molo, fifty people were charged with various traffic offences. Those apprehended were rivers, matatu conductors, passengers and boda bodas.
In Makueni, the few matatus on the road increased fares by between 50 and 100 per cent.
Many commuters and matatu operators complained that the reinstatement of Michuki rules caught them unawares and asked for more time to make the necessary changes.
Riders who took advantage of the crisis, did not bother about some of the rules like having helmets and reflective jackets.
Report by Agewa Magut, Brian Okinda, Stephen Muthini, Winnie Atieno, Charles Lwanga, Mary Wambui, Eunice Murathe, Pius Maundu, Justus Ochieng', Victor Otieno, Judith Achola, Derick Luvega, Caroline Mundu, Benson Amadala, Vitalis Kumutai, Magati Obebo, Elisha Otieno, Gastone Valusi and Shaban Makokha.