Chris Grayling suggested motorists should consider buying a low-emission vehicle rather than spending their money on a diesel.
His intervention follows reports the Government is considering a scrappage scheme for diesel cars to improve air quality.
The reported scheme would see drivers offered a cash incentive for replacing an old diesel car with a low-emission vehicle.
Asked whether motorists should hesitate before buying a diesel, Mr Grayling told The Daily Mail: “People should take a long, hard think about what they need, about where they’re going to be driving, and should make best endeavours to buy the least polluting vehicle they can.
“I don’t think diesel is going to disappear but someone who is buying a car to drive around a busy city may think about buying a low-emission vehicle rather than a diesel.”
Concern over the impact of diesel cars on nitrogen dioxide (NO2) levels were raised by the Volkswagen emissions scandal in September 2015.
It emerged 11 million Volkswagen diesel vehicles around the world had been fitted with software to release fewer smog-causing pollutants during tests than in real-world driving conditions.
Analysis by the Department for Environment, Food and Rural Affairs (Defra) found NO2 is estimated to be responsible for 23,500 deaths in the UK each year.
Government advisory panel the Committee on Climate Change believes 9% of new car sales should be electric by 2020 for the UK to meet its legal obligation to cut greenhouse gas emissions by 80% by 2050 compared with 1990 levels.
In 2016 the market share of new car sales for alternatively fuelled vehicles was 3.3%, up from 2.8% the previous year.
In June last year then-transport secretary Patrick McLoughlin said it had been a mistake for former Labour chancellor Gordon Brown to slash taxes on diesel.
Mr Brown reduced duty on low-sulphur fuel in 2001, which contributed to an increase in annual diesel car registrations from 3.45 million to 8.2 million.
A Government report published in April 2016 showed that diesel cars being sold in the UK emit an average of six times more nitrogen oxide in real-world driving than the legal limit used in official tests.
The Department for Transport investigation found all of the 37 top-selling diesel cars tested exceed the legal limit required for laboratory tests when driven for 90 minutes on normal roads.
Ministers insisted no laws had been broken by the manufacturers as cars are only required to meet the lab test regulations.
A scrappage scheme to boost the motor industry ran from May 2009 until March 2010, offering motorists £2,000 to scrap an old car for a new model.