Chief Cabinet Secretary Yoshihide Suga told a hastily arranged news conference late on Tuesday that Japan "received information from Qatar that Mr Jumpei Yasuda had been released".
Yasuda was last heard from in Syria in 2015.
Japanese prime minister Shinzo Abe said on Wednesday he was "relieved" to hear of the release, but that the government still needed to confirm the man's identity.
Speaking to reporters, Abe thanked Qatar and Turkey for their cooperation in freeing the hostage.
"I'm relieved to hear the information," Abe said. "We want to confirm whether the man is Mr. Jumpei Yasuda as soon as possible."
Suga said earlier the government was making checks to confirm the released man was Yasuda. But it was highly likely that was the case, he said, adding that the journalist's his wife had been notified.
Yasuda started
reporting on the Middle East in the early 2000s.
He was taken hostage in Iraq in 2004 with three other Japanese nationals, but was freed after Islamic scholars negotiated his release.
His most recent trip to Syria was in 2015 to report on his journalist friend Kenji Goto, who was taken hostage and killed by the Islamic State of Iraq and the Levant (ISIL, also known as ISIS) armed group.
Contact was lost with Yasuda after he sent a message to another Japanese freelancer on June 23, 2015.
In his last Twitter post two days previously, Yasuda had 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 have been released in the past year.
In one of them released in July, the man said he was in a harsh environment and needed to be rescued immediately.