TOKYO — Prime Minister Shinzo Abe of Japan offered to resign a year ago if evidence emerged linking him to a sweetheart land deal. No such evidence ever surfaced, allowing him to ride out the scandal and hang on to power.

But a government report released on Monday suggests that some crucial evidence may have been deleted — and that has put Mr. Abe back in the hot seat. An internal investigation by the Finance Ministry concluded that unidentified officials tampered with official documents related to the land deal by deleting references to Mr. Abe’s wife and senior members of his party.

The findings caused an uproar in Japan, where critics called for the finance minister, Taro Aso, to resign. At a news conference on Monday, Mr. Aso, a former prime minister, said he would stay in his post. But analysts said the latest revelations would be politically damaging for Mr. Abe as he prepares to seek a third term.

“This materially changes the outlook for Abe’s future,” said Tobias Harris, a Japan analyst at Teneo Intelligence, a political risk consultancy based in New York. “The basis for him seeking a third term is evaporating.”