The government admitted on Monday that Finance Ministry documents related to a contract on the sale of a state land lot to private school operator Moritomo Gakuen at a deep discount were altered in and after late February a year ago in the wake of the revelation of the controversial deal.
Copies of documents seen by Reuters showed that references to Abe, his wife and Aso were removed from finance ministry records of the sale of state-owned land to a school operator with ties to Abe's wife.
Finance Minister Taro Aso said Monday that an investigation by the ministry and prosecutors has found 14 instances of alterations.
Opposition lawmakers have also demanded that Akie Abe and Sagawa be called in to testify.
Abe has campaigned to inject patriotism into schools: during his first term as prime minister in 2006 the law was revised to include nurturing "love of country" as an educational goal. Aso suggested that the document tampering was limited to a handful of bureaucrats. She told Kaoike the donation was from Shinzo Abe, he said.
Questions about the sale of land - sold at a huge discount that officials said was for clean-up costs - have dogged Abe since it became public a year ago. It said one document originally noted that the school operator was involved with a powerful pro-Abe political lobby, Nippon Kaigi, of which Abe was vice chairman, but that comment had later been deleted.
In a parliamentary hearing Monday, Finance Ministry officials confirmed that a reference to Akie Abe having recommended the land deal was deleted from a document after the scandal surfaced.
The doubts have also sparked calls for Mr Aso to quit, but the Finance Minister said on Friday he would not step down. The complex scandal appears to have dented Abe's popularity as he attempts to win re-election as head of his ruling party in September.
Aso is vital to the stability of his administration and key to his bid for a third term as LDP president in a September party election, which would pave the way for him to be Japan's longest-serving prime minister. The "heinous" alterations were "conducted systematically", said Yuichiro Tamaki, head of the center-right opposition party Kibo no To, or Party of Hope.
Shinzo Abe acknowledged the new revelations "could undermine trust in the entire government" and added: "I deeply apologise to the people", said a report in The Guardian. "They make light of the legislature and are utterly unacceptable".
On Friday, National Tax Agency chief Nobuhisa Sagawa abruptly resigned over his remarks in parliament about the case. Mr Sagawa headed the ministry division that submitted the documents before he was tapped as tax agency chief in July - an appointment critics saw as a reward for his efforts to diffuse the issue with his statements to Parliament past year.
"It is inconceivable that the bureaucrats on the spot had such authority [to alter the documents]", media quoted Shigeru Ishiba, an LDP lawmaker who has made no secret of his desire to challenge Mr Abe in the party race, as saying on the weekend.
Abe, 63, swept back to power in December 2012 promising to revive the economy and bolster Japan's defense.
The conservative Yomiuri newspaper and public broadcaster NHK both reported declines in support ratings for Abe's Cabinet in polls released Monday. Non-support rose to 42% and 80% said that the matter had not been handled appropriately.