Delfin Lorenzana also told a security forum in Singapore that President Rodrigo Duterte has been under pressure to declare martial law in at least three southern islands where jihadists operate, but he did not think there was a need.
The defence secretary (minister) said the companies which employed two recently freed Indonesians had paid a ransom of 20 million pesos (USD 400,000).
He did not identify the captives but the Philippine military said two Indonesian hostages were freed last month by militants from Abu Sayyaf, which has pledged allegiance to the Islamic State group.
Security analysts had said ransom was paid for the release by the Abu Sayyaf last year of a Norwegian hostage, although the Philippine and Norwegian governments denied it.
Lorenzana told the Fullerton Forum organised by the International Institute for Strategic Studies that 25 kidnap victims are still being kept in the southern island of Jolo.
Jolo is a stronghold of the Abu Sayyaf, which is known to behead its victims if ransoms are not paid. The group decapitated a Malaysian in 2015 year and two Canadians last year.
"It seems that the whole of the community are into it, not everybody but a major part of the community are benefitting from the ransom," he said.
The government is trying to "convince the companies and the families not to pay ransom because everytime they pay ransom they make the kidnappers stronger," he said.
"They have more money to distribute to the communities and they have more money to procure all the gadgets that they need -- cellphones, firearms and even materials to manufacture improvised explosive devices."
He said many Filipinos wanted the president to declare martial law over South Tawi Tawi, Jolo and Basilan islands.
But this would be "very controversial" and Duterte was not considering the idea.
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