Sir Keir Starmer is having “ongoing discussions” with the Mayor about alternatives to the Ulez expansion and how drivers are compensated for upgrading their cars.
The Labour leader on Thursday said his party had “an obligation to look at other options” when questioned about the controversial scheme.
Sadiq Khan expanded the Ulez to the London boundary at the end of August in a bid to help clean up the capital’s toxic air hotspots.
It sees the drivers of older, more polluting cars face a £12.50 daily charge to use their vehicles.
Sir Keir told BBC Radio London: “[Sadiq Khan] of course is in a difficult place because there is a legal obligation to take action to reduce air pollution so you can’t sit this out.
“I do want to look at other options. I do understand this is expensive. It imposes cost on people in a cost of living crisis. So we do need to look at how it is implemented.
“The way I look at this is I’ve got two young kids - a 15-year-old boy and a 12-year-old girl - and I don’t give them dirty water to drink and I don’t want them breathing in dirty air.”
But he added: “We have an obligation to look at what other options are out there and how we can help further.
“That’s an ongoing discussion between me and the Mayor. We speak regularly.”
A spokesman for Sir Keir said measures that would help support Londoners and people living in the Home Counties, such as scrappage schemes, were being discussed.
Mr Khan launched a £160million scrappage scheme earlier this year, which is funded entirely by City Hall. But it is not available to drivers living just outside the London boundary.
Other cities, such as Bristol and Birmingham, have received financial support from the Government for clean air programmes.
The Ulez expansion policy was blamed for Labour losing the Uxbridge by-election in July.
The Labour London Assembly member for Ealing and Hillingdon lost the backing of a number of his party’s local activists.
He will have to fight other party figures in order to remain Labour’s candidate for the west London seat at next year’s City Hall elections.
Drivers have also staged multiple protests since the scheme came into force in outer London boroughs.
The Met said is investigating nearly 800 reports of Ulez cameras being stolen or vandalised since April 1.
A source close to Mr Khan said: “The Mayor agrees with Keir that schemes such as the Ulez aren’t right for everywhere.
“As he has reiterated, what is right for London may not be right for rest of the country. There are no alternative options that would have the same level of impact in London when it comes to cutting toxic air.
“The Government has provided scrappage funding in other cities implementing clear air zones, including Birmingham, Bristol and Portsmouth, but has not given a single penny to London and the Home Counties.
“This Government should support Londoners like they have other parts of the country, as Keir has outlined."
