Local media reported that more than 20 senior military, defence and government officials were being held at the MNLF's camp near Panamao town on Jolo island, 950 km south of Manila but senior military sources, who declined to be identified, would only confirm three hostages.
Dolorfino, a Muslim convert who had flown to Jolo for talks with the MNLF, told reporters by text message that he was safe.
"Sorry I can't comment. Just wait for the policymakers to speak," he said.
A military spokesman declined to comment.
The governor of Sulu, an archipelago that includes Jolo, said a local MNLF commander, Habier Malik, had refused to allow Dolorfino, Santos and 11 others to leave on Friday until their leader, Nur Misuari, was released from detention in Manila.
Misuari was jailed in 2002 for rebellion after the breakdown of a peace deal the MNLF signed with the government in 1996.
The Philippines is a largely Catholic country but has a sizeable Muslim minority in the south, where a decades-old conflict between Islamic separatists and government troops has killed over 120,000 people.
Dolorfino, former deputy commander of the Philippines's southern forces, is the highest-ranked Muslim in the armed forces.