According to exit polls by public broadcaster NHK, Mr Ishiba’s Liberal Democratic Party is certain to lose its majority in the 465-seat chamber, the most powerful of Japan’s bicameral parliament.
It is not yet clear whether his ruling coalition with junior partner Komeito can retain a majority.
The results could weaken Mr. Ishiba’s grip on power, and if he cannot push his party’s policies through parliament, he may have to find a third partner.
Mr. Ishiba took office on Oct. 1, replacing his predecessor, Fumio Kishida, who resigned after failing to reassure the public about widespread kisha practices among Liberal Democratic Party politicians.
Mr Ishiba immediately called early elections in an attempt to shore up his support using his outspoken reformist image.
Voting began Sunday morning across Japan, where 1,344 candidates, including a record 314 women, are vying for the post.
Mr Ishiba has aimed to retain 233 seats for the ruling coalition between the LDP and its Buddhist-backed junior partner Komeito, a majority in the 465-seat lower house – the most powerful of Japan’s bicameral parliament.
In his final speeches on Saturday in Tokyo, Mr Ishiba apologized for his party’s misuse of funds and promised to “start again as an equal, fair, modest and honest party”.
He said only the ruling LDP coalition can responsibly govern Japan with its experience and reliable policies.
Once a popular politician known for his criticism of even his own party’s policies, Mr. Ishiba has also received support for his cabinet for weeks.
The largest opposition party, the Constitutional Democratic Party of Japan, is led by centrist leader Yoshihiko Noda, who was briefly prime minister during the 2009-12 LDP ouster.
Mr. Noda’s party is expected to make significant gains. He said Sunday’s election was a rare chance to change the government, which would be the most effective political reform, even though his party was having trouble finding other opposition groups to cooperate with.
At a Tokyo polling station early Sunday, a number of voters said they were weighing the corruption scandal and economic measures.
A 77-year-old man said his biggest concern was rising prices and wondered if the LDP should win despite the mistakes. Another resident, in her 60s, said she would vote in hopes of making a difference.
Analysts suggest Mr Ishiba may fall short of his seat target, although his LDP is expected to remain the leading party in Japan’s parliament, as voters are skeptical about the opposition’s ability and inexperience.
Losing his majority would mean Mr Ishiba would struggle to establish policies and could face calls from his party for a replacement ahead of next summer’s upper house elections, experts say.