Mehrtens was freed and picked up by a joint team in the Nduga area, undergoing health check-ups and a psychological examination in Timika regency, the Indonesian police said in a statement.
Indonesian police spokesman Bayu Suseno said Mehrtens will be flown to Jakarta in an air force plane and is estimated to arrive at the Halim Perdanakusuma airbase in east Jakarta about 8pm local time (11pm AEST).
Mehrtens was abducted by independence fighters after he landed a small plane in Papua. (AP PHOTO)
Indonesia's Metro TV earlier showed Mehrtens speaking tearfully to his family by phone. He then made an appearance at a press conference and seemed to be in good spirits.
Mehrtens did not appear to suffer any post-traumatic stress although he had lost a lot of weight, Bambang Trisnohadi, a lieutenant general with the Indonesian military, told the press conference.
A faction of the West Papua National Liberation Army kidnapped Mehrtens in February 2023, after he landed a small commercial plane in the remote, mountainous area of Nduga.
I'm grateful Phillip Mehrtens has been released after more than 19 months in captivity. My appreciation to all those in Indonesia and New Zealand who have supported this positive outcome for Phillip and his family.— Christopher Luxon (@chrisluxonmp) September 21, 2024
NZ Prime Minister Christopher Luxon said on social media platform X he was grateful Mehrtens had been released.
"My appreciation to all those in Indonesia and New Zealand who have supported this positive outcome for Phillip and his family," Luxon said.
"His family will be absolutely over the moon," NZ Foreign Minister Winston Peters told reporters in Auckland.
A range of New Zealand government agencies had been working with Indonesian authorities and others towards securing Mehrtens' release, Peters said earlier in a statement.
The pilot was undergoing health checks before being flown to Jakarta. (AP PHOTO)
Indonesia's leader said Mehrtens' welfare had been the main concern throughout the talks.
"Through the long process of negotiation, with patience not to do it repressively, our priority has been the safety of the pilot," President Joko Widodo said in televised remarks.
In August, another New Zealand pilot, Glen Malcolm Conning, was killed by separatist rebels in Papua after landing his helicopter in a remote area, authorities said at the time.