Mehrtens was freed and picked up by a joint team in the Nduga area and was undergoing health check-ups and a psychological examination in Timika regency, the Indonesian police said in a statement.
Mehrtens was handed over early on Saturday to the Cartenz Peace Taskforce, a joint security force set up by the Indonesian government to deal with separatist groups in Papua.
"We managed to pick him up in good health," taskforce spokesman Bayu Suseno said.
A faction of the West Papua National Liberation Army, led by Egianus Kogoya, kidnapped Mehrtens in February 2023 after he landed a small commercial plane in the remote, mountainous area of Nduga.
"We are pleased and relieved to confirm that Phillip Mehrtens is safe and well and has been able to talk with his family. This news must be an enormous relief for his friends and loved ones," said New Zealand Foreign Minister Winston Peters.
A range of New Zealand government agencies had been working with Indonesian authorities and others towards securing Mehrtens' release, Peters said in a statement.
The Indonesian police are due to hold a press conference later on Saturday.
"We are prioritising approach through religious leaders, church leaders, traditional leaders and Egianus Kogoya's close family to minimise casualties and maintain the safety of the pilot," said Indonesian Brigadier General Faizal Ramadhani, head of Cartenz 2024 Peace Operations.Â
With AP