The government action comes after months of anger over a housing affordability crisis in major cities including Barcelona, news portal Travel Mole reports.
The Spanish Consumer Rights Ministry said many listings have violated record-keeping rules, citing discrepancies such as missing licence numbers and owner declarations.
Spaniards have increasingly blamed short-term rentals on housing shortages and surging rental costs.
Consumer Rights Minister Pablo Bustinduy said the clampdown will address the general ‘lack of control and illegality’ in the holiday let market.
“No more excuses," he said. "Enough with protecting those who make a business out of the right to housing in our country."
The move is mostly targeting what it calls "illegal listings" in Madrid, Barcelona and parts of Andalusia.
Airbnb is appealing the action and has filed a court motion.
Official data shows there are more than 320,000 licensed rental properties in Spain, but officials say there are many more operating illegally.
The Consumer Rights Ministry first opened an investigation into Airbnb late last year.
The housing shortage crisis has been at the centre of anti-mass tourism protests across Spain in the past year.
Barcelona has already taken measures to alleviate the problem, with plans to remove around 10,000 licensed short-term rental apartments within the next three years.