Plans to reduce emissions will see highly-pollutant vehicles banned from city centres in Scotland by 2020.
There will be a further ambition to phase out traditionally-fuelled vehicles by 2032.
However, fresh information has shown 17 out of 25 ministerial vehicles use diesel, which has been described as “embarrassing” and “disappointing”.
Yannick Read, from the Environmental Transport Association, said: “It is extremely disappointing that two thirds of Scottish ministerial vehicles are diesel-powered, but we suspect this ‘do as we say and not as we do’ approach to air pollution is echoed by many areas of government around Britain, especially at a local level.
“So we would urge all departments to practice what they preach and invest in alternative fuel vehicles.”
Scottish Labour environment spokeswoman Claudia Beamish urged the Government to consider replacing the diesel cars in favour of greener transport.
She said: “To have more than two-thirds of the ministerial fleet of cars operating on diesel could give the impression ministers are complacent about the impact diesel fuel has on our air quality.”
Scottish Liberal Democrat environment spokeswoman Mariam Mahmood added: “This is embarrassing – SNP ministers should be leading by example.”
The Scottish Government wants the country to phase out petrol and diesel-powered vehicles by 2032 in favour of alternative fuels and hybrids.
It has also committed to introducing low emission zones into the four biggest cities by 2020.
Scotland’s ministerial fleet includes 17 diesel Skoda Superbs, two cars powered by petrol and six hybrid/petrols.
The non-diesel range includes a Lexus RX450h, two Mitsubishi Outlander PHEVs and a VW Passat PHEV among others.
A spokesman for EV Association Scotland congratulated the Scottish Government and Transport Scotland for the work they had done to promote greener travel.
He added: “Scotland has excellent charging infrastructure compared with other UK areas, but stopping for a 30-minute charge after driving 150 miles may not be ideal for a minister on a mission.
“Until there is an alternative fuelled vehicle that takes this up to 250 miles, it would be unfair to criticise. After all, Scotland is quite a large country and not all journeys will be in the Central Belt.”
Figures from the RAC Foundation in December showed use of electric vehicle charge points in Scotland increased by 43 per cent in 2017.
A Scottish Government spokesman said: “We continually look for ways to ensure the government car service is delivered in the most cost-effective manner, offering the best deal to the taxpayer.
“We are committed to leading by example on tackling climate change and to reducing our carbon emissions and replacing fossil-fuelled vehicles with plug-in vehicles, where appropriate.
“In line with our procurement strategy, we evaluate existing technologies to assess their operational suitability for future use within the government car service and wider Scottish Government fleet.
“As part of this, we recently trialled a new fully electric vehicle to establish its suitability for potential future use. There was no cost for this trial.”