"On the recommendation of the crisis centre of the Federal Interior Public Service, all our metro and light railway stations... Will stay closed today. This is a precautionary measure," Brussels transport operator STIB said on its website.
"Buses will be running but some trams will be affected by this measure," added the network, which said a decision would be taken "in consultation with relevant authorities and the police, day by day, whether to reopen the stations".
The alert remains at level 3 for the rest of the country.
The centre urged citizens to avoid crowded areas such as concerts and transport hubs in Belgium's capital, which is also home to the European Union and NATO headquarters, and recommended that authorities in the Brussels region "consider cancelling major events" including scrapping first and second division football matches this weekend.
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The suspect, who has not been identified, is the third to be charged in Belgium over the deadliest terror attacks in French history after Hamza Attou and Mohammed Amri were charged this week with aiding fugitive suspect Salah Abdeslam on the night of the attacks.
Brussels resident Abdeslam, whose brother Brahim blew himself up at a Paris bar, is believed to be in Belgium and is the subject of a huge manhunt.
The fugitive is closely linked with the alleged Paris attack ringleader Abdelhamid Abaaoud, who was killed in police raid in the French capital on Wednesday.