In a separate operation, the ministry said police seized 8,000 guns and rifles yesterday and arrested five Spaniards suspected of buying disused weapons to recondition them and put them on the black market for international extremist and organized crime groups.
The ministry said that the two people arrested today in Spain's North African enclave city of Ceuta had undergone a long process of radicalization and formed part of a group that was advancing toward carrying out terror activities.
It said police were searching six houses and premises in the city, which is bordered by Morocco on one side and the Mediterranean Sea on the other.
The ministry said Spanish police have arrested 180 suspected jihadi activists over the past two years, many of them in Ceuta.
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Spain has been one step below maximum security alert since attacks in Europe and elsewhere in 2015.
The ministry said yesterday's operation stemmed from an investigation into the guns used in the suspected jihadi attack on a Jewish museum in Brussels in 2014 that killed four people. It wasn't immediately clear if police found that the arms used in the attack came from the Spanish group.
The arrests were made in several towns across northern Spain.