A second key official stepped down over the scandal, the finance minister confirmed late Friday, as the damaging issue refuses to go away.
Police are investigating the death of the official in Kobe in western Japan and suspect he committed suicide, with some media reporting a suicide note had been found.
A police spokesman contacted by AFP could not immediately confirm the reports.
The unidentified official, who was found dead on Wednesday, was at the heart of a scandal over the cut-price sale of government-owned land to a close friend of Abe, the reports said.
Separately, Finance Minister Taro Aso told reporters that another senior official involved in the scandal, Nobuhisa Sagawa, had decided to step down after lawmakers and taxpayers demanded his resignation.
Sagawa was promoted to head the tax agency in July, after holding a post overseeing the finance ministry division that negotiated the deal.
"Sagawa is a capable individual," said Aso.
"He said he wants to resign to take responsibility for the troubles caused."
The scandal has dogged Abe since it first emerged last February, though the prime minister has consistently denied any wrongdoing and his approval ratings remain solid.
According to local media, the land was sold for around one tenth of its market value, and the kindergarten had announced plans to name Abe's wife Akie the honorary principal of a primary school being built on the same plot.
Abe says his wife had only "reluctantly" accepted the post of honorary principal and had since "resigned."
The allegation has paralysed parliament in recent days, with some opposition lawmakers boycotting debates.
The opposition has accused ministry officials of hiding some key documents and colluding to cover up the scandal.
Aso said he had told his ministry staff to come up with conclusions early next week but stressed he himself had no plans to step down over the scandal.
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