A finance ministry employee in the western region where the school is located was found dead at his home on March 7 and police are investigating it as a suicide, the Kyodo and Jiji news agencies reported.
The latest twist in the land sale scandal has seen the former head of the ministry's Kinki bureau, who had come under fire for allegedly making false remarks about the sale to the Diet previous year, resign on Friday from his subsequent job as head of the National Tax Agency.
The scandal over the heavily discounted sale of land to Moritomo Gakuen, a school operator with ties to Abe's wife, contributed to a decline in Abe's public popularity previous year.
The scandal regained fresh momentum last week with opposition parties turning up the heat after the Asahi newspaper said some documents about the land sale might have been doctored.
Telephone calls seeking ministry comment went unanswered.
A Japanese finance ministry official linked to the cronyism allegations dogging Prime Minister Shinzo Abe has been found dead, local media said on Friday.
On the day of Mr Sagawa's resignation, press reports said the police were investigating as a possible suicide the death of an official at a Finance Ministry bureau that handled the land deal. But falling support could complicate his bid for a third term as Liberal Democratic Party leader in a September party vote. The government's chief spokesman said he had been notified about the death but declined to give details.
Local authorities said foul play is not suspected, adding though the man is linked to the sale of deeply discounted land to Moritomo Gakuen, a school foundation with links to the first lady, the suicide can not be attributed entirely to the school scandal.
He was responsible for the 2016 sale of a plot of land in Osaka to the right-wing operator of a kindergarten at a price well below market value, according to reports.
Abe says his wife had only "reluctantly" accepted the post of honorary principal and had since "resigned".