Police should always respect those rights, Bathan said, "otherwise, their good intentions will remain as such simply because they have blundered."
The Indonesians said they were carrying copies of the Koran and not weapons on a trip to the southern Philippines to spread Islam. They said they did not have passports because they thought they were not required.
A Filipino militant arrested with the Indonesians was freed on bail but disappeared, Bathan said.
The militant was believed to have rejoined his armed group, the brutal Abu Sayyaf, on southern Jolo island but was reportedly killed by his comrades on suspicion he had turned into a government spy, a senior Philippine anti-terrorism official said on condition of anonymity because of the sensitivity of his work.
U.S.-backed military offensives have crippled the al-Qaida-linked Abu Sayyaf in recent years, but it remains a key security threat. Washington lists the group as a terrorist organization.
The Philippine police and military say the Abu Sayyaf provided sanctuary and training grounds to Jemaah Islamiyah members in an alliance that started in the mid-2000 and has since been weakened by U.S.-backed Philippine offensives.