The 100th day of Prime Minister Yukio Hatoyama’s administration was marred by disgrace. On Thursday, two former secretaries to Mr. Hatoyama were indicted for falsifying political funds reports. The case is not linked to corruption, but it casts serious doubt over the transparency of the Hatoyama office’s handling of political funds. It deals a blow to the prime minister himself, since he and his Democratic Party of Japan won the general election in August with calls for a change in Japan’s politics.

One of the secretaries, who actually handled political donations, was charged, among other things, with inflating the amount of political donations that Mr. Hatoyama’s political funds management organization received from individuals during 2004-2008 — from the actual amount of some ¥101 million to some ¥308 million. In doing so, he is suspected of having listed 270 fictitious donors or padded the sum of small donations (¥50,000 or less) whose donors need not be identified.

The other secretary, who was chief accountant and charged with gross negligence for failing to notice the falsification, received a summary court order to pay a fine of ¥300,000. It is suspected that part of the some ¥1.26 billion that Mr. Hatoyama’s mother provided him from 2002 was disguised as donations from individuals. He has not disclosed how the money was used.

Mr. Hatoyama himself submitted a written explanation to prosecutors. Although he was not questioned by them and managed to escape indictment due to insufficient evidence of his involvement, his political responsibility is heavy.

On Thursday, Mr. Hatoyama said that since he entrusted everything to his secretaries, he did not know anything about the falsification of reports about political donations. He also said he “really and absolutely did not know” anything about the provision of funds by his mother. It will be hard for people to believe that.

Mr. Hatoyama should remember his earlier statement: A politician should be punished if his or her secretary commits a crime. With large political liabilities, he will have a hard time steering clear of harsh questions in the coming Diet session.