Katsuyuki Kawai tendered his resignation, saying he wanted to avoid damaging public trust in the justice system.
His wife, Anri Kawai, who won her first seat in an Upper House election in July, allegedly paid campaign staff members a daily allowance that exceeded the legal limit, according to reports that first surfaced Wednesday.
Last Friday, Trade Minister Isshu Sugawara resigned just one month after being appointed, following accusations that he broke campaign laws by giving gifts to voters that included expensive melons and crabs, as well as offering a supporter's family money.
Upper House lawmaker Masako Mori has been appointed to take over as justice minister. Hiroshi Kajiyama, a former regional revitalization minister and district representative, has been appointed trade minister.