Trains in several Belgian cities including Brussels were stopped for up to an hour on Friday and some stations were evacuated after police received hoax bomb threats by telephone.
Police said stations in Louvain and Antwerp had to be evacuated to be swept for bombs, while the central station in Brussels was checked by a dog trained to find explosives.
"Service is back to normal now," a police spokesman said.
Belgium, which hosts NATO and European Union institutions, relaxed security on Thursday after a two-week state of alert prompted by the uncovering of an apparent Islamist plot to free an al Qaeda suspect from jail.
Fourteen suspected Islamic militants had briefly been detained and Brussels cancelled its traditional New Year fireworks display because of a perceived threat.