Matsuoka, 62, known as a fervent lobbyist for farmers in his district, hanged himself Monday as he was set to face questioning in parliament over a bid-rigging scandal.
Prime Minister Shinzo Abe will appoint former vice defence chief Norihiko Akagi, Jiji Press, Kyodo News and major national dailies said, quoting unnamed government sources.
His confirmation ceremony was set for Friday at the Imperial Palace.
The 48-year-old Akagi, currently a lower house lawmaker, served as vice chief at the Defense Agency under Abe's predecessor Junichiro Koizumi.
Akagi, a graduate of the University of Tokyo's law school, had worked at the agriculture ministry before being elected to parliament in 1990.
He is also a grandson of six-time farm minister Munenori Akagi.