Some 2.1 million Audis affected worldwide include 1.42 million in western Europe, with 577,000 in Germany, and almost 13,000 in the US.
Czech-based Skoda said 1.2 million of its cars were involved, but has yet to give a country or model breakdown.
Separately, German prosecutors started a probe against VW's former boss.
Former chief executive Martin Winterkorn will be investigated over "allegations of fraud in the sale of cars with manipulated emissions data," German authorities said on Monday.
The Audi models affected  include the A1, A3, A4, A5, A6, TT, Q3 and Q5 models, a spokesman told the Reuters news agency.
VW said last week that 11 million cars within the group could be affected.
The scandal was revealed after the US Environmental Protection Agency found that some diesel cars were fitted with devices that could detect when the engine was being tested and could change the car's performance to improve results.
The German company apologised for breaching consumers' trust, and on Friday announced that Matthias Mueller was replacing Martin Winterkorn as chief executive. Mr Mueller promised a "relentless" investigation to uncover what went wrong.
There were also unconfirmed reports on Monday that senior R&D heads working across the car group had been suspended. Reuters said the suspensions involved staff from the Audi, Porsche and the VW brands.
Meanwhile, Volkswagen shares continued to fall, closing down 7.3%. They are now down about a third since the scandal broke.
The scandal has badly tarnished VW's name, left it exposed to up to $18bn in US fines, and wiped a third off its stock market value in a week.
German authorities have demanded that VW set out a timeline by 7 October on how it will ensure its diesel cars meet national emission standards without using cheat technology.
There were widespread German media reports at the weekend that the government ignored warnings two years ago that VW was using the software. However, on Monday, a government spokesman denied this.
11 million
Vehicles affected worldwide
â‚¬6.5bn Set aside by VW
$18bn Potential fines
No. 1 Global carmaker in sales
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Audi and Skoda say they have a total of 3.3 million cars fitted with the software that allowed parent company Volkswagen to cheat US emissions tests.