Japan's Justice Minister Midori Matsushima has resigned, hours after the resignation of Trade and Industry Minister Yuko Obuchi.
Ms Matsushima had been accused by the opposition of violating election laws.
Ms Obuchi is alleged to have misused funds from her political support groups and other donations.
Correspondents say the resignations are a major setback for PM Shinzo Abe, who wants to bring more women into the top levels of government.
Mr Abe said he took responsibility for having appointed both women, and that they would be replaced within a day. Both are members of his governing conservative Liberal Democratic Party (LDP).
Ms Obuchi, 40, was one of five women appointed by Mr Abe in his cabinet reshuffle last month and was tipped by some as a future prime minister.
But allegations emerged last week that her staff had misused thousands of dollars of campaign funds.
Ms Obuchi has not acknowledged personal wrongdoing, but at a televised press conference on Monday, she said she was resigning because "we cannot let economic policy and energy policy stagnate... because of my problems".
"I take seriously the impact I have caused," she said. She also apologised for being unable to contribute to key goals set by Mr Abe, including economic recovery and "a society where women shine".
Hours later Mr Abe announced that Ms Matsushima, 58, had also resigned.
She had distributed paper fans carrying her image and policies at a festival in her constituency, said NHK.
The opposition Democratic Party filed a criminal complaint against her on Friday, and demanded her resignation, saying this was an apparent violation of election law and rules on usage of political funds.
The BBC's Japan correspondent Rupert Wingfield-Hayes says that this is not the end of Mr Abe's problems concerning his new female ministers.
Eriko Yamatani, minister in charge of the North Korean abduction issue, was shown in photographs with members of an ultra-nationalist group accused of hate speech against Japan's ethnic Korean community.
Mr Abe's first term as prime minister in 2006-2007 saw a string of scandals amongst his ministers, eventually leading to his own resignation for health reasons after just one year in office.