The two-seater plane went missing yesterday after it took off from an airfield in Ibaraki prefecture.
The wreckage of the plane was found at a nearby golf course early Sunday with the two victims, aged 59 and 57, in the cockpit, a local police spokesman said.
They were unconscious and were later confirmed dead, the spokesman said, adding that the two were believed to have been travelling in the plane. Police and aviation authorities were investigating the cause of the crash.