Johnson's party was ousted in Wandsworth - a low-tax Conservative stronghold since 1978, which had been one of main opposition Labour Party's main targets.
The Conservatives also said they had lost control of the borough of Barnet, which has been held by the party in all but two elections since 1964.
"This is a warning shot from Conservative voters," said Daniel Thomas, the Conservative leader of Barnet council.
The overall tally due later on Friday will offer the most important snapshot of public opinion since Johnson won the Conservative Party's biggest majority in more than 30 years in the 2019 general election.
The ballot is the first electoral test for Johnson since he became the first British leader in living memory to have broken the law while in office. He was fined last month for attending a birthday gathering in his office in 2020, breaking social distancing rules then in place to curb COVID's spread.
Early results showed the Conservative Party had lost 92 council seats. The main opposition Labour Party had gained 23 seat and the Liberal Democrats 42 seats.
A poor set of results will increase pressure on Johnson, who has been fighting for his political survival for months and faces the possibility of more police fines over his attendance at other lockdown-breaking gatherings.
The results will decide almost 7000 council seats, including all those in London, Scotland and Wales, and a third of the seats in most of the rest of England.
Johnson upended conventional British politics in the 2019 general election by winning and then promising to improve living standards in former industrial areas in central and northern England.
But the loss of Wandsworth and Barnet symbolises the way that Johnson, who won two terms as mayor of London, has lost his appeal in the capital. His support for Brexit cost him support in London, where a majority of voters supported staying in the EU in the 2016 Brexit referendum.
The outcome outside the capital is likely to be less clear-cut. The Conservatives lost overall control of councils in Southampton, Worcester and West Oxfordshire.
But the party have not done as badly as some polls had predicted. One poll in the run up to the elections said the Conservatives could lose about 800 council seats.
John Curtice, a professor of politics at the University of Strathclyde, said early trends suggested the Conservatives were on course to lose about 250 seats.
However, some local Conservative council leaders called on Johnson to resign after the party's poor performance, which they blamed on him being fined and the cost-of-living crisis.
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