Col. Bernardus Robert, spokesman of the APEC Joint Security Command, declined to provide details about the journalists but said there was a zero tolerance policy for any threats.
"We will not tolerate any possibility, even small, of threats against the heads of state and the implementation of APEC Summit should not be disturbed," he said.
The journalists approached Aquino on the sidelines of the meeting.
"Will you apologize to Hong Kong people for their real tragedy?" a woman reporter asked, TV footage showed. "Will you give an answer? It has been three years," she said.
"So you are ignoring Hong Kong people, right?" another reporter asked.
Aquino did not reply to their questions. Now TV footage showed an APEC staff member telling the reporters: "You ambushed one of our visitors."
In Beijing, Foreign Ministry spokeswoman Hua Chunying said China supported the Hong Kong government's efforts to remain in close contact with the Philippines about the hostage incident.
"We urge the Philippine government to pay high attention to the requirements and concerns of the families of the victims, take concrete and effective measures and work out a proper solution as soon as possible," Hua said in a statement released late Monday.
In 2010, eight Hong Kong tourists and their guide were killed after being held hostage for a day inside a tour bus by a dismissed Manila police officer. The crisis ended with a botched police rescue.
Aquino has expressed regret over the bloodshed but repeatedly said he considers the issue closed and that it was not appropriate for the Philippine government to apologize because the state was not responsible. However, families of the victims have continued to press for an official apology and compensation.
The Now TV footage showed another APEC staff member telling one of the reporters: "You know that the decency (includes) not screaming. You do understand that?"
The reporter is heard answering, "I am asking, I'm not screaming, OK?" The staffer went on to tell him, "Now out!"
Gatot S. Dewabroto, a member of Indonesia's APEC Organizing Committee, said the credentials of nine Hong Kong journalists were revoked for behavior that was "excessive, disrespectful and disturbing the event."
He said the decision was not made at the request of the Philippines. The reporters are barred from entering the conference venues but can cover the APEC meetings from outside, he said.
Edwin Lacierda, Aquino's spokesman in Manila, said the APEC organizers took "appropriate measures."
"The Indonesians felt that it was not civil and it was not courteous," he said.
Leaders of the 21-member Asia-Pacific Economic Cooperation forum along with thousands of business leaders, officials and journalists are meeting amid tight security on this tropical island in eastern Indonesia for an annual summit.