Papua New Guinea police are guarding Indonesia's consulate compound in the border town of Vanimo after its gate was rammed by a vehicle and a boat damaged.
Police say they had brought a suspect in for questioning following Tuesday night's attack.
The Indonesian Consular-General, Kristanyo Hardojo, has told PNG's newspaper, The National, that the identity of the attackers was not known.
But sources in Vanimo told the newspaper that relatives of a local businessman who disappeared on the Indonesian side of the border last month could have been responsible for the attack.
Relatives of Constant Nere, who moved from Papua province to PNG more than 30 years ago during high tensions over the Indonesian takeover, fear he was kidnapped on his first trip back over the border.