Latvia's Road Traffic Safety Directorate (CSDD) said attack also affected 200,000 companies.
The attack reportedly secured information last week such as first and last names, payment details, vehicle licence plates and the address registered on the day the service was provided.
Latvia has a population of around 1.9 million. It was initially unclear who was behind the incident.
Prime Minister Andris Kulbergs said a cyberattack originating from another country could not be ruled out, according to the Leta news agency.
Latvia's cybersecurity authority and the CSDD warned the stolen data could be misused by fraudsters.
Kulbergs ordered an investigation into the incident and criticised the CSDD management for informing him about the data theft only after a delay.
"I have to say that I am unpleasantly surprised by a certain IT-security infantilism that exists in some regulatory authorities and government institutions," the prime minister said.
He referred to a previous hacker attack on the state forestry administration in June.
Two "serious cyber incidents" occurring within a short period were a clear signal that additional security measures were needed, he said.
"This is now quite literally a matter of national security," Kulbergs said.
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