Copies of documents seen by Reuters showed that references to Abe, his wife and Aso were removed from finance ministry records of the discounted sale of state-owned land to a school operator with ties to Abe's wife, Akie.
Abe has repeatedly denied he or his wife did favors for school operator Moritomo Gakuen, which bought the land, and had said he would resign if evidence were found that they had.
The scandal emerged past year and concerns the sale of land to a supporter of Abe at a price said to be around one tenth of its market value.
Yuichiro Tamaki, leader of the opposition Kibo no To (Party of Hope), said the issue is no longer a problem that only involves the ministry, but is a sign of the Abe administration's cover-up habits.
News that the ruling Liberal Democratic Party was briefed by a government official that some documents related to the land deal had been altered "raised uncertainty over whether the Abenomics economic policy will continue", an official at a foreign exchange margin trading service firm said.
Abe said Aso will not step down.
Also on Friday, media said police were investigating as possible suicide the death of a finance ministry official whose local office had handled the land sale.
Abe told reporters he wanted Finance Minister Taro Aso to fulfill his responsibility by clarifying the facts of the alterations. The doubts have also sparked calls for Aso to resign.
The Mainichi Shimbun has reported the documents were doctored to be "coherent" with a speech made in parliament by the head of the tax agency Nobuhisa Sagawa, who stepped down on Friday over the scandal.
Some LDP members said the saga could undermine the party.
The original documents included the names of several politicians, which were deleted before being submitted to lawmakers, mass circulation Yomiuri Shimbun and other media reported Monday. It was a rare comeback for the conservative lawmaker, who quit abruptly in 2007 after a year in office marked by scandals in his cabinet, a deadlocked parliament and ill health.