Despite protests from Hong Kong's main journalist group, President Benigno Aquino's spokesman also said the journalists had "crossed the line" by aggressively questioning Aquino about a hostage siege in Manila that left eight Hong Kong people dead in 2010.
"We deemed it improper for media to act that way, as they didn't talk normally but they were very demonstrative, like they were protesting," said Gatot Dewa Broto, the Indonesian communications ministry official in charge of the media centre in Bali for the Asia-Pacific Economic Cooperation forum.
They were free to remain in Bali, but could no longer access the media center or venues being used for the summit.
Hong Kong media said the journalists and technicians were from Now TV, RTHK and Commercial Radio.
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A journalist at Now TV said three of its reporters were briefly detained by Indonesian police following the incident.
"They were detained for four hours today afternoon. There were three of them, including one text reporter and two cameramen, being detained," Daphne Lo, senior reporter of Now TV, told AFP.
Now TV footage showed the journalists shouting "So you're ignoring the Hong Kong people, right?" and "Have you met CY Leung" as they tried to extend their microphones over Aquino's entourage.
He did not answer the questions, and APEC staff then intervened to admonish the journalists.
Sham Yee-lan, chairwoman of the Hong Kong Journalists' Association, said Aquino's government had "yet to provide a satisfactory explanation" for why the eight Hong Kongers had died in a botched police rescue and the journalists in Bali were doing their job.
Now TV said its journalists were "only engaged in normal reporting duties" and urged intervention from the Hong Kong government, which is one of APEC's 21 members.