TOKYO — The highest-ranking civil servant in Japan’s Finance Ministry offered his resignation on Wednesday amid swirling accusations that he had sexually harassed several female journalists.

At a news conference, the official, Junichi Fukuda, 58, the administrative vice minister, said allegations that he had made sexually suggestive remarks to the women were “not factual.”

Still, Mr. Fukuda’s resignation, which was accepted by Taro Aso, the finance minister, was a small sign that Japan might be joining the international reckoning of the #MeToo movement, spurred by widespread accusations of sexual harassment and assault.

Two days earlier, Mr. Fukuda threatened to sue Shukan Shincho magazine, which originally reported the accusations. On Wednesday, he also vowed, “I am going to dispute it in court.”