It was unclear whether Ishiba's Liberal Democratic Party would be able to secure a majority in parliament alongside its long-time coalition partner, the Komeito Party.
Ishiba, 67, took office on 1 October after being elected LDP leader last month, and called snap elections within days of taking office.
The self-confessed defence "geek" and model aircraft maker has made it his goal to win a coalition majority in the election.
Failure to achieve this goal would seriously undermine his position in the LDP and mean finding other coalition partners or heading a minority government.
Voters in the world's fourth-largest economy are under pressure from rising prices and the fallout from the party's slush fund scandal that helped sink former Prime Minister Fumio Kishida.
NHK predicts the LDP will win between 153 and 219 seats, short of the 233 needed for a majority in the 465-seat parliament.
Together with Komeito, which is predicted to have 21-35 seats, the coalition will have between 174 and 254 seats.
The Constitutional Democratic Party (CDP), led by former Prime Minister Yoshihiko Noda, will win between 128 and 191 seats, up from 96, the broadcaster predicted.
If the official results are confirmed, the LDP's loss of the majority would be its worst result since it lost power 15 years ago.
In Japan's previous general election in 2021, the LDP won an independent majority with 259 seats in the influential lower house. "Komeito had 32.
Opinion polls before the election suggested that the LDP would not be able to achieve a majority and even that the ruling coalition might also end up with an insufficient majority.
Ishiba promised to revitalise backward rural areas and tackle the "quiet emergency" associated with Japan's declining population through family-friendly measures such as flexible working hours.
But he has backtracked on issues including allowing married couples to bear separate surnames. He also appointed only 2 women as ministers in his cabinet.
He supported the creation of a NATO-style regional military alliance to counter China, although he agreed that this "will not happen overnight".
The LDP is one of the most successful parties in the democratic world - a one-size-fits-all party that has been in power for almost all but 4 of its 69 years.
In 1993, the LDP was thrown out of power for the first time after the dramatic bursting of Japan's asset bubble in the 1980s and a corruption scandal.
The last time it was out of power was between 2009 and 2012, when it was replaced for three chaotic years by the centre-left HDP, which had to deal with the Fukushima nuclear disaster in 2011 | BGNES
