Masaichi Yamada, who runs a fish-processing company, was arrested in the northern Japan port of Kushiro early Tuesday when the frozen corpse - still fully clothed - was uncovered.
"The suspect maliciously strangled the victim with a string-like object at their home and abandoned her body in the freezer at his working place," a spokesman for police in Hokkaido told AFP by telephone.
It was not immediately known when the murder took place, the official said, adding the woman would have been 71 years old if she was alive today.
Yamada reportedly confessed to the police he killed his wife during an argument at their home "sometime between 2002 and 2006" and carried the body by car to the factory.
Police searched the factory after the dead woman's brother said he had not been able to contact his sister for several years.