Jonila Castro, 21, and Jhed Tamano, 22, had been working with coastal communities opposed to reclamation activities in Manila Bay when they disappeared on September 2 in Bataan province, near the capital Manila.
The Philippines is one of the most dangerous countries in the world for land and environmental defenders, with 11 killed in 2022, according to watchdog Global Witness.
Rights groups launched an investigation in the days after Castro and Tamano's disappearance.
They alleged the women had been violently abducted, possibly by "state actors", apparently in relation to their activism.
On September 15, nearly two weeks after the pair's disappearance, the National Security Council (NSC) and police announced at a news conference that Castro and Tamano were being held in a safe house after they sought help from authorities.
They denied the women were activists and said allegations by "leftist organisations" that they had been abducted was "fake news" and an "elaborate hoax".
"They were portrayed as environmentalists. They are not environmentalists but leftist organisers. They left the movement of their own free will," NSC spokesman Jonathan Malaya told reporters at the time.
On Tuesday, however, Castro and Tamano offered a different version of events at a news conference hosted by the government's National Task Force to End Local Communist Armed Conflict, which was set up by former president Rodrigo Duterte.
- 'Threatened to kill us' -
The task force has frequently accused government critics of being communist sympathisers, without providing any evidence.
The practice, known as "red-tagging", can result in the arrest, detention or even death of the person targeted. It has continued under President Ferdinand Marcos Jr, who succeeded Duterte in 2022.
Castro and Tamano appeared to go off script during the news conference at the Plaridel Municipal Hall in Bulacan province.
"The truth is we were abducted by the military via a van," Castro said.
"We were obliged to surrender because they threatened to kill us. That's the truth. We did not want to be in the custody of the military."
Castro said the statement they signed was "not true".
"We had no choice during that time. We want to show today the state's blatant fascism towards activists, who only want to fight for Manila Bay," she said.
Recordings of the news conference were widely shared on X, formerly known as Twitter.
Links to the videos were later removed from the Facebook pages of Plaridel municipality and the task force.
Karapatan, an alliance of local rights groups, said the women's statements showed official claims they had surrendered to authorities were "all lies and hogwash".
"We demand the safe release of Jhed Tamano and Jonila Castro now, and not a second longer," Karapatan secretary general Cristina Palabay said.
Military spokesman Medel Aguilar declined to comment other than by saying: "We will wait for the report of our field unit there."
Malaya did not respond immediately to AFP's request for comment.
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