In hotly awaited parliamentary testimony beamed live on national television, Nobuhisa Sagawa said only his office took part in altering key documents relating to a controversial land sale.
"This is an issue only for the finance bureau (of the ministry) ... therefore we never reported outside the finance bureau ... not to mention reporting to the prime minister's office," said Sagawa, 60.
He said neither Abe nor his cabinet secretary or finance minister had ordered the alterations.
Sagawa's testimony came as fresh polls showed public support for Abe's government plunging by double digits, apparently due to the scandal, amid opposition calls for the prime minister to resign.
However, the official declined to answer detailed questioning about how and when documents were altered, saying he was under criminal investigation.
The scandal revolves around the 2016 cut-price sale of state-owned land to a nationalist school operator who claims ties to Abe and his wife Akie.
The row deepened when the finance ministry admitted official records of the sale were altered, with references to Abe, his wife, and Finance Minister Taro Aso scrubbed.
Abe has apologised repeatedly, but denies any wrongdoing.
On Monday he pledged a "thorough investigation so that everything can come to light".
Sagawa was head of the finance ministry department that oversaw the sale in 2016, and was promoted to head Japan's tax agency the following year.
As the scandal made national headlines, he stepped down, and the opposition has sought repeatedly to bring him before parliament to testify.
Several times last year, Sagawa told MPs the price of the land "was properly calculated" and stressed there was no evidence of political pressure in the sale.
Official documents relating to the sale were apparently altered to make them consistent with his testimony, according to the finance minister.
Sagawa's testimony Tuesday was the first time he has been officially summoned to address parliament under oath.
A career bureaucrat who began working at the finance ministry in 1982, Sagawa stepped down earlier this month, with some experts saying Abe's government hoped the resignation would draw a line under the scandal.
But the opposition has continued to press Abe and his cabinet to take responsibility for the scandal, as well as pushing for Akie Abe to testify to parliament a request the premier's ruling party has so far rejected.
The opposition says Sagawa's testimony "is only a first step towards revealing the whole truth" about the scandal.
The affair took a tragic turn earlier in the month when an official from the finance ministry apparently involved in the scandal took his own life.
The row has battered Abe's popularity and called into question whether he can still win a party leadership contest this September and become Japan's longest-serving prime minister.
His approval rating plunged by 14 percentage points to 42 percent this month, according to a survey published Monday by the business daily Nikkei, with his disapproval rating at 49 percent.
The liberal TV Asahi's poll Monday said public support dropped by 11.7 percentage points to 32.6 percent.
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