A Japanese freelance journalist who went missing three years ago in Syria has said he is safe and well in Turkey after being released by his captors.

Jumpei Yasuda spoke in brief videotaped comments in English carried online on Wednesday by the Japanese broadcaster NHK. He said he was now safe after being held for 40 months.

Yasuda has been at an immigration centre in southern Turkey near the border with Syria since he was freed on Tuesday. Japanese embassy officials had met Yasuda at the centre, said Japan’s foreign minister, Taro Kono.

The Japanese prime minister, Shinzo Abe, thanked the Turkish president, Recep Tayyip Erdoğan, in a phone call on Wednesday for the “rescue” and safe arrival in Turkey of Yasuda, a Turkish presidential source said.

Yasuda started reporting on the Middle East in the early 2000s. He was taken hostage in Iraq in 2004 with three other Japanese nationals and was later freed after Islamic clerics negotiated his release.

In 2015 he went to Syria to report on the death of his friend Kenji Goto, a journalist who was taken hostage and killed by Islamic State.

Contact was lost with Yasuda after he sent a message to another Japanese freelancer on 23 June 2015. In his last tweet two days earlier, he said his reporting was often obstructed and that he would stop tweeting his whereabouts and activities.

Several videos showing a man believed to be Yasuda were released in the past year.