Patrick McLoughlin said that it had been a mistake for former Labour chancellor – and Prime Minister – Gordon Brown to cut taxes on diesel.
In an interview with the Evening Standard, McLoughlin said: "We have got to look at that. It is something the chancellor will need to look at in due course.
"It's something that we've got to address. We are addressing it through the government's air quality strategy, and by putting money into public transport like the Elizabeth line."
The decision by Brown to cut taxes on diesel had led to a rise in the number of cars releasing nitrogen oxide across the UK. The duty on low sulphur diesel was cut by 3p in Brown's 2001 Budget.
It is estimated that 9,400 Londoners die prematurely each year due to the level of pollution in the city.
Last year the government reaffirmed the UK's commitment for almost all cars and vans to be zero emission by 2050 at the Paris climate conference.
Read more: McLoughlin says Gatwick is still an option
"Electric cars are greener and cheaper to run and we are making them more affordable, spending more than £600m between 2015 and 2020 to support the uptake and manufacturing of ultra-low emission vehicles here in the UK," transport minister Andrew Jones said last year.
But in April this year ministers rejected a diesel scrappage scheme, whereby owners would get a cash incentive to trade their car in, as "ineffective and expensive".
In the same month, a Department for Transport study found the top 37 diesel models are producing many times more pollutants than claimed by tests undertaken in laboratories.
In March, think tank Policy Exchange said government should increase the first year Vehicle Exercise Duty (VED) rate for new diesel cars by up to £800 to reflect the higher levels of air pollution they cause compared to petrol cars, which could generate £500m a year to fund the scrappage scheme.