The two ministers were among five women Abe named to his Cabinet in a reshuffle early last month. Their resignations may help to control the damage to his relatively high popularity ratings, but are a blow to efforts to promote women in politics and business as part of economic revival policies.
Yuko Obuchi, daughter of a former prime minister and a rising star in the ruling Liberal Democratic Party, resigned early Monday as trade minister, saying she needed to focus on an investigation into discrepancies in accounting for election funds. She did not acknowledge any wrongdoing.
Justice Minister Midori Matsushima resigned after the opposition Democratic Party of Japan filed a criminal complaint against her over distribution of hand-held fans or "uchiwa." Matsushima also faces complaints over using parliament-provided housing while keeping security guards at her private residence in downtown Tokyo.
Speaking to reporters shortly after he accepted Matsushima's resignation, a sombre Abe told reporters he was also responsible because he appointed the two women to his Cabinet.
"I deeply apologize to the public," Abe said.
Within hours, Abe named replacements, choosing Yoichi Miyazawa, 64, a former finance ministry official as trade minister. Miyazawa, from Hiroshima, served as a secretary years ago to his uncle, former Prime Minister Kiichi Miyazawa.
Abe chose Yoko Kamikawa, 61, a female lawmaker who has worked on demographic issues, as the new justice minister.
Abe's first term in office, in 2006-2007, was marred by gaffes and resignations by his Cabinet ministers and he stepped down, citing ill health. His current term has been smoother, particularly in the first year as the stock market soared along with his popularity ratings.
Pressure for faster action on economic reforms has risen, however, as the recovery faltered following a 3 percentage point increase in the sales tax in April.
Political funding scandals are a chronic problem in Japan and key factor behind the revolving-door politics of recent decades.
"These rules are in place precisely because vote-buying using gifts used to be very common in Japan and still is according to some accounts in the rural areas," said Koichi Nakano, a politics professor at Tokyo's Sophia University.
The types of gifts and sums of money at the centre of the latest allegations are relatively trivial compared with the record of previous governments. In one case, a stash of gold bullion pulled from an LDP lawmaker's offices. But the rules are well-known, and possible violations by a minister of justice did not set well, Nakano said.
Two other female Cabinet members known as Abe's close allies on the right have been criticized for suspected ties with racist groups, marring his efforts to encourage Japan to accept more women in leadership positions.
Abe's broad gender agenda includes pushing companies to promote more women, expanding spaces for day care, and other measures intended to help encourage improved opportunities for Japan's highly educated but underemployed female workforce. Such moves are vital for economic growth as Japan's population declines and ages.
Obuchi, who as trade minister was overseeing the cleanup and decommissioning of the wrecked Fukushima Dai-ichi nuclear power plant, said a thorough investigation into the problems with her campaign funds would interfere with her duties.
"I apologize for not being able to make any contributions as a member of the Abe Cabinet in achieving key policy goals," Obuchi said.
The Cabinet resignations are the first for Abe since he took office in late 2012.
The opposition DPJ lost power to Abe's conservative Liberal Democratic Party in late 2012 and is seeking whatever leverage it can against the LDP's overwhelming parliamentary majority.
Hence the focus on such issues as presents of leeks, baby clothes, theatre tickets and fans by lawmakers to their supporters. The "uchiwa" distributed by Matsushima reportedly cost a mere 80 yen (75 cents) each, but are a possible violation of the election law.
Matsushima contends they should be allowed as campaign "leaflets."
Analysts said Obuchi's troubles stem from a campaign apparatus set up decades ago when her grandfather and then her father were in office.
She apologized for funding irregularities, though she said she had found no evidence of alleged personal use of campaign funds that were paid to a company run by a relative. But discrepancies in the accounting for several years have raised a "major doubt," she said.
"This is my own fault and I will focus on investigating so that I can regain trust from my supporters as soon as possible," Obuchi said.