Manila's reaction came two days after Beijing said it had "destroyed" an intelligence network set up by a Philippine espionage agency and had arrested three Filipino spies.
The espionage dispute comes as the two countries confront each other over disputed territory in the South China Sea and as tensions rise over the Philippines' security ties with ally the United States.
There have also been several arrests in the Philippines this year of Chinese citizens accused of spying on military camps and vessels.
A report by Chinese state broadcaster CCTV on Thursday included what appeared to be a recorded confession by a Philippine national it said had been identified as one of the suspected spies.
The CCTV report said the man had lived in China for a long time and had been found spying near military facilities.
However, the National Security Council (NSC) in Manila said the supposed confessions "appear to be scripted, strongly suggesting that they were not made freely".
The arrests "can be seen as retaliation for the series of legitimate arrests of Chinese agents and accomplices", it said in a statement.
The NSC said the three unidentified Filipinos were among 50 former recipients of scholarships offered by China's Hainan National University.
"They are ordinary Filipino citizens with no military training who merely went to China at the invitation of the Chinese government to study," it said.
"They are law-abiding citizens with no criminal records and were vetted and screened by the Chinese government prior to their arrival there."
It urged Beijing to "respect their rights and afford them every opportunity to clear their names in the same way that the rights of Chinese nationals are respected here in the Philippines".
The NSC also said the spy agency mentioned by Chinese media as having recruited one of the suspects did not exist.
The Philippine foreign affairs department said on Friday it was "providing all necessary assistance, including appropriate legal support".
Beijing's embassy in Manila issued a travel warning to its citizens last week about frequent "harassment" from Philippine law enforcement agencies.
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