The investigation revealed "the threat of serious attacks that would target several emblematic places in Brussels and be committed during the end-of-year holidays," the prosecutor's office said.
The two suspects were arrested following searches Sunday and Monday in the Brussels area, the Liege region and Flemish Brabant, the office said. The announcement did not say whether the suspects were male or female.
One was charged with acting as the leader and recruiter of a terrorist group planning to commit terrorist offenses, the other with participating in a terrorist group's activities as a principal actor or co-actor, the prosecutor's office said.
Six people were taken in for questioning, but four were released, the office said.
The prosecutor's office said no additional details would be made public, but that the probe was not connected to the November 13 attacks in Paris, in which numerous suspects, including presumed ringleader Abdelhamid Abaaoud and fugitive Salah Abdeslam, had connections to Belgium.