Indonesia Coordinating Minister for Political, Security and Legal Affairs, Luhut Pandjaitan says the kidnapping of two Indonesians near the Papua New Guinea border was a criminal act.
Antara news agency quotes him saying it had nothing to do with politics.
On Saturday, the Indonesian consulate in Vanimo in PNG reported that two Indonesian citizens had been kidnapped by unknown armed people in Skopro in Papua and are being held in Skoutio village in Sandaun Province, just three hours awaye.
Mr Pandjaitan says PNG and the Indonesian Government representatives are continuing to negotiate with the hostage takers.
He says there has been no talk of ransom or an operation to free the hostages, with both government waiting to see the outcome of the negotiations.
They were taken by armed men on Wednesday while cutting wood in Skopro in the sub-district of Arso Timur in the district of Kerom, Papua bordering Papua New Guinea, which is a three-hour walk from Skoutio.