A dozen arrests were made and about 100 searches carried out across Portugal against a "criminal network with international connections which made money illegally from contraband diamonds and drug trafficking".
The army chief of staff issued a statement saying the military's role as couriers was being investigated.
"What we are looking into now is the possibility that some soldiers taking part in the National Detached Force in CAR were used as couriers in the trafficking of diamonds, gold and drugs," suspected of being transported on military planes, the statement said.
The probe followed a tipoff from within the Portuguese force in CAR, which was informed in December 2019 of the possible involvement of soldiers in trafficking.
Portuguese media said the dragnet targets a dozen suspects, including active duty troops and ex-soldiers.
Defence Minister Joao Gomes Cravinho described the situation as "deeply regrettable", adding that the UN had been informed last year.
"An inquiry is under way to determine what happened and to take the exemplary measures that have to be taken," said President Marcelo Rebelo de Sousa.
Portugal has 180 soldiers deployed in the former French colony as peacekeepers with the UN mission there. Lisbon has contributed to the force since 2014.
The Central African Republic is rich in gold, diamonds and other minerals but crippled by poverty, conflict and sectarian violence.
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