Abe, in power since late 2012, is in little danger of losing his job, but his popularity has taken a hit in the midst of the latest shady dealings claims.
They come a few months after the conservative premier was forced to deny connections to a controversial director of a school which had purchased government land at a huge discount -- and counted Abe's wife as its honorary principal.
The claims, originally reported by the Asahi newspaper last month, centre on documents that suggested the education ministry was pressured to grant approval for a new veterinary school run by one of Abe's old university buddies.
The friend, Kotaro Kake, allegedly wanted to open his school in a special economic zone so that he could bypass the ministry's cumbersome regulations.
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In response to the claims, the education ministry launched a probe last month but it quickly closed the investigation and said it "could not confirm the existence of the documents".
"I'm taking this result seriously," Education Minister Hirokazu Matsuno told reporters this week.
Today, the Cabinet Office also said it had unearthed similar papers, but questioned whether they proved Abe intended to pressure education ministry bureaucrats.
"There was no such instruction from the prime minister," top government spokesman Yoshihide Suga said Friday.
Earlier this year, Abe denied claims he made a donation to the school at the centre of the land scandal.
The school's director Yasunori Kagoike had gained notoriety for operating an Osaka kindergarten that instills pupils with ultra-nationalist views.