"At this stage we think it is a terrorist incident," a police spokesperson Hashmat Stanikzai told AFP, describing the incident as an abduction.
No group has so far claimed responsibility for the killings.
A spokesperson from the interior ministry also confirmed the incident, saying the victims were from India, Macedonia and Malaysia.
The three men were working for a logistics company in the capital.
The incident happened after the group left their office with a car and driver Thursday.
Just over an hour later their bodies were found in what appeared to be a different car by authorities in the rural outskirts of Kabul.
"They had been shot inside the car," said Bahar Mehr with the interior ministry.
Taliban claim to defeat Islamic State fighters in north Afghanistan
Kabul is plagued by criminal gangs who stage abductions for ransom, often targeting foreigners and wealthy locals, and sometimes hand them over to insurgent groups.
Kidnapping of Afghans and foreigners is also common across Afghanistan where swathes of the country are infested with militant groups or criminal gangs.
In August 2016, gunmen wearing military uniforms kidnapped two professors of the American University of Afghanistan in the heart of Kabul.
The two, American Kevin King and Australian Timothy Weeks, appeared looking haggard in a Taliban hostage video, with the insurgents later adding that King was in poor health.
Aid workers in particular have increasingly been casualties of a surge in violence in recent years.
Prominent Afghan militia commander among four killed in suicide attack
Afghan civilians have borne the brunt of the grinding conflict that began after the 2001 US-led invasion toppled the Taliban regime.
Militant attacks and suicide bombs were the leading causes of civilian deaths in the first half of 2018, a recent UN report showed.
While the Taliban is Afghanistan's largest militant group and holds or contests more territory than any other insurgent outfit, the Islamic State has repeatedly demonstrated its ability to carry out devastating attacks in urban areas.
Taliban claim to defeat Islamic State fighters in north Afghanistan
The incident comes a day after more than 150 Islamic State fighters surrendered in northern Afghanistan move that Afghan security forces and the Taliban hailed as the end of the extremist group in the north of the country.
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