Police arrested Veerasak Iampongsa, 39, in Nakhon Si Thammarat, 780 kilometres south of Bangkok, on Sunday, Crime Suppression Division Deputy Commander Police Colonel Prasobchok Prommoon said.
Japanese authorities had sought cooperation through the Thai Attorney General's Office, he said.
The case's statute of limitations will expire on March 14, after which it could not be tried, he said.
No hearing date has been set but the trial and any prison sentence would be in Thailand, which has no extradition treaty with Japan, Prasobchok said.
Veerasak allegedly murdered Japanese citizen Awaji Megumi, 33, in early 1993 then fled to Thailand.//DPA