The Moritomo Gakuen scandal, which first surfaced in February a year ago and pushed down Abe's support ratings, has drawn fresh attention since a major Japanese daily reported on March 2 that the ministry documents had been doctored to remove descriptions stating the discounted land sale price was "exceptional".
The sale was clinched at a price well below market value amid allegations that the high-level connections helped grease the deal.
The unprecedented doctoring of public documents has prompted an emboldened opposition to step up calls for Finance Minister Taro Aso's resignation and dial up attacks on Abe.
The widening scandal threatens to damage Abe's hopes of securing a third term as leader of the Liberal Democratic party (LDP) - and continuing as prime minister - when the party holds its leadership vote in September.
He said he feels keenly responsible, and wants to apologize to the Japanese people.
"I would like the finance ministry to make all efforts to rebuild the organisation so we can regain trust and prevent such a thing from happening again", Mr Abe said.
"If this is true, isn't political responsibility unavoidable?" said Akira Nagatsuma, a senior lawmaker in the opposition Constitutional Democratic Party of Japan, on Sunday.
The developing political scandal is raising doubts about Abe's ability to continue to pursue his economic policies, including monetary easing. The head of the National Tax Agency, Nobuhisa Sagawa, who was in charge of overseeing the sale, has also quit. Adding that the finance ministry division has instructed changes to the documents to match testimony in parliament. The school operator described her visiting the site and telling Moritomo Gakuen to "go ahead" with its plans, as the site was a "good" one.
Colts Possible Free Agent Targets: CB Dominique Rodgers-Cromartie
He was set to have an $8.5 million cap hit in 2018, and the Giants will save $6.5 million on their salary cap by releasing him. Rodgers-Cromartie has 30 career interceptions but had none in 2017 after matching his career high with six in 2016.
Patriots QB Tom Brady Shave His Head For Cancer Research
Granite Telecommunications pledged to give over $5 million to the cancer institute if 1,000 people shaved their heads or beards. As many Patriots and National Football League fans know, Brady's mother Galynn is a cancer survivor.
U.S. may exclude some countries from trade tariffs
Canada and Mexico have objected to tying the tariff issue to NAFTA, as it essentially stacks the deck in America's favor. Trump's sudden push for the tariffs last week triggered fears of a global trade war and rattled financial markets.
Opposition politicians suspect the school won a sweetheart deal.
But this time the nation is troubled with its Prime Minister Shinzo Abe and his alleged involvement in an elementary school scandal.
Text saying Moritomo Gakuen and the ministry office had arrived at a deal "after negotiations on price and other matters" was deleted as well.
The scandal, linked to records of a sale of state-owned land to a school operator, have plagued the PM for more than a year. But officials pledged to "get the Financial Bureau chief's permission to sell", that text said. "It's not the case that the whole Ministry of Finance was involved".
The scandal now threatens to engulf Abe's government after bureaucrats conceded they forged documents in an apparent bid to hide the couple's involvement.
Sagawa headed the ministry division that submitted the documents before he was tapped as tax agency chief in July, an appointment that critics saw as a reward for his efforts to diffuse the issue with his statements to parliament previous year.
On Monday, Aso blamed bureaucrats for the suspected cover-up.
However, this month the Asahi newspaper reported that the documents related to the transaction had likely been changed from the originals.