The statement came after the Hong Kong government announced yesterday it would impose diplomatic sanctions against the Philippines because of its "unacceptable" failure to apologise.
"The Philippine Government regrets the Hong Kong SAR Government's implementation of sanctions against the Philippines," foreign affairs spokesman Raul Hernandez said in a statement.
However he said the Philippines "is not prepared to consider" an apology.
Rather, the Philippines would reiterate its "deepest regret and condolences", while providing more compensation to the survivors and the victims' relatives.
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They are currently able to stay 14 days without a visa.
Leung described the move as the "first phase of sanctions" and said the government may take more action if it thought it could be "effective" in securing an apology over the hostage-taking.
Hong Kong has been infuriated by the Philippines' refusal to apologise for the incident in August 2010, in which a former local police officer hijacked a Manila tour bus in protest at his sacking.
Philippine President Benigno Aquino has consistently rejected Hong Kong's demands for an apology, saying the tragedy was caused by the hostage-taker.
The Philippines has already provided undisclosed financial compensation, with the money donated by private individuals.
Without specifically referring to money, Hernandez said the Philippines had responded to appeals for "compassion" from Hong Kong "without equivocation and in a most generous manner" and that more compensation was on its way.
Hernandez indicated that the Philippines had believed that recent pledges of more compensation, and their imminent delivery, had resolved the issue.
"To bring the issue to its final conclusion, the Philippines remains committed to manifest compassion for the victims and their families and is ready to turn over the additional tokens of solidarity from the Filipino people," he said.