Ambassador to Jakarta Rafael Seguis said the guard, whose identity was withheld pending investigation, was picked up for questioning along with two other suspects.
The guard was among those earlier arrested by the Indonesian police following the blast but was later released.
Seguis said the same guard was arrested again last week after authorities discovered new evidence linking him to the bombing.
Aside from the guard, authorities have arrested two farmers following a raid in a village in Manado, on Indonesia’s Sulawesi island.
Commenting on the arrest, Seguis said the conduct of the investigation by the Indonesians is much better now, compared to the probe on the August 2000 bombing of the Philippine Embassy in Jakarta.
Until now, Seguis said, Indonesian authorities have yet to resolve the bombing which critically injured Ambassador Leonides Caday.
Authorities believe the Manado blast is connected to the Bali car bomb attack later that same night which left almost 200 people dead and scores of others, mostly foreigners, seriously injured.N