But on Monday, the Finance Ministry submitted an 80-page report to the governing Liberal Democratic Party, admitting that ministry bureaucrats had deleted portions of 14 documents related to the land sale, including ones containing the name of Mr. Abe’s wife, Akie Abe, and her alleged remarks.
Mr. Aso suggested that the document tampering was limited to a handful of bureaucrats.
“Only some of the Finance Ministry’s employees were involved in the alteration” of the documents, he said. “It’s not the case that the whole Ministry of Finance was involved. But it’s regrettable if the trust for the whole ministry is lost.”
The prime minister apologized shortly after the disclosures became public.
“As head of the administration, I deeply apologize,” Mr. Abe said in brief remarks to reporters on Monday afternoon. He added that he hoped an investigation would “uncover the whole truth.”
The most dramatic admission was that bureaucrats had removed Mrs. Abe’s name and alleged comments from a description of a meeting between Finance Ministry officials and administrators of the Moritomo education group, which operates a kindergarten where children recite a 19th-century patriotic royal decree and are taught that some history textbooks in Japan and elsewhere in Asia wrongly characterize the country’s wartime atrocities.
According to the deleted remarks, a Moritomo administrator told Finance Ministry officials in Osaka that when he showed Mrs. Abe, a onetime honorary principal of a planned Moritomo elementary school, the location of the land, Mrs. Abe said: “It’s good land. Please go ahead.” The land was slated for construction of a new school in Osaka, Japan’s third-largest city.
The report also showed that Finance Ministry officials had removed the names of several Liberal Democratic lawmakers from the land sale documents, as well as a reference to Nippon Kaigi, a prominent right-wing pressure group of which Mr. Abe and other influential conservative politicians are members.
At the news conference on Monday, Mr. Aso said bureaucrats altered the documents between February and April last year. Last February, Mr. Abe said he would resign as prime minister and a member of Parliament if evidence emerged showing that he or his wife was connected to the discounted land sale to Moritomo Gakuen.
When reporters asked Mr. Aso on Monday whether the bureaucrats had acted to protect the Abes, Mr. Aso said that in his judgment, Mrs. Abe had nothing to do with the case.
Last week, Nobuhisa Sagawa, former chief of the bureau within the Finance Ministry that oversaw the land sale, resigned from his current post as tax agency chief. Earlier this month, a Finance Ministry employee in the Osaka branch office that had dealt with the land sale committed suicide.
Opposition lawmakers have long questioned Mr. Abe’s denials of involvement in the land sale. But as news of the altered documents emerged, even members of Mr. Abe’s own party were skeptical of the explanation that bureaucrats acted independently.
Newsletter Sign Up
Thank you for subscribing.
An error has occurred. Please try again later.
You are already subscribed to this email.
In comments to the Nikkei newspaper, Shinjiro Koizumi, a rising star within the party and a son of Junichiro Koizumi, a former prime minister, said blaming bureaucrats was the equivalent of “cutting off a lizard’s tail.”
“If the falsifications are true, we need to tell the truth to people,” Mr. Koizumi said. “We have to take it not only as an administrative issue, but as one that affects all politics.”
And in a speech on Sunday, Shigeru Ishiba, one of Mr. Abe’s rivals within the Liberal Democratic Party, said he did not believe that bureaucrats had the power to alter documents without political direction.
“Unless we clarify who did this, trust for the Liberal Democratic Party will be shaken,” Mr. Ishiba said.
Polls have shown Mr. Abe’s popularity declining as media reports suggested that document tampering had taken place. A survey over the weekend by the right-leaning Yomiuri Shimbun found the cabinet’s approval rating had dropped below 50 percent for the first time in five months. That same poll found that 80 percent of respondents said the government was mishandling the Moritomo case.
Analysts said Mr. Abe’s ratings were likely to decline further at a time when his government is struggling to gain exemptions from steel and aluminum tariffs imposed by President Trump and to grapple with the foreignpolicy implications of Mr. Trump’s decision to meet with North Korea’s leader, Kim Jong-un.
“The political authority or prestige of the Abe administration will decrease drastically because of this scandal,” said Jiro Yamaguchi, a professor of political science at Hosei University in Tokyo.
Critics of Mr. Abe said the way the disclosures had slowly emerged showed the weakness of the Japanese news media and the conservative tilt of the government bureaucracy.
The bureaucracy is “very secretive, arrogant and authoritative,” said Koichi Nakano, a political scientist at Sophia University in Tokyo. He added that because the opposition had been so divided, it had not been potent enough to challenge Mr. Abe.
Analysts said the slow drumbeat of the scandal would inevitably weaken Mr. Abe and his agenda. His most cherished long-term goal — to try to change the pacifist clause in the country’s Constitution — is now probably compromised.
And even if Mr. Abe can hold off calls for resignation now, his chances for re-election in a party leadership vote in September have diminished.
“Without clear signs of his being involved, I think it’s hard to assume that he’s going to be forced out,” Mr. Harris said.
“But I think there’s enough here now that as you approach the preparation for the L.D.P. elections in September, there is going to be a sense in the party of ‘You know what, enough of the drama and more than a whiff of scandal. It’s time for someone clean and a little more low key,’ ” he added.