The queue at one filling station was one kilometre long, according to local media, which said nearly 3,000 were already dry across the country.
An estimated 800 filling stations were out of petrol in the region around the capital Lisbon and 400 around the northern city of Porto.
The union which represents a majority of Portuguese truck drivers who haul dangerous materials went on strike on Monday seeking a wage hike and special protections.
The government on Tuesday ordered a certain number of drivers back to work in order to ensure a minimum service to airports, ports, emergency services, public transport and 40 percent of filling stations in the Lisbon and Porto regions as the country begins marking a three-day holiday weekend for Easter on Friday.
“The minimum service will be enlarged if necessary,” Prime Minister Antonio Costa told lawmakers in a debate on Wednesday.
Negotiations held on Tuesday made no progress.
Download our app and read this and other great stories on the move. Available for Android and iOS.