The winner of Wednesday's party poll to succeed unpopular Prime Minister Yasuhide Suga, who is not seeking re-election after just one year in office, is almost certain to become premier because of its majority in parliament's lower house.

Japan's next prime minister must call a general election due in weeks and faces the task of rebuilding an economy staggering from the COVID-19 pandemic.

Kono, 58, a US-educated former defence and foreign minister is seen as a maverick but driven by public popularity, while former foreign minister Fumio Kishida, 64, is saddled with a bland image but has a stronger support base from party members in parliament.

"I did all I had to do. Next is just to wait for a call," Kono told reporters before the first round vote, according to Kyodo.

Kono got a total of 255 votes, while Kishida had 256.

Kishida and Kono defeated in the first round two female candidates: former internal affairs minister Sanae Takaichi, 60, an ultra-conservative; and Seiko Noda, 61, from the party's dwindling liberal wing.

With his support in tatters ahead of the election, Suga surprisingly announced earlier this month that he would step down after only a year as the LDP leader.

With masks on, the LDP's parliamentary members, including Suga and former prime minister Shinzo Abe, were voting in the runoff in the ballroom of a Tokyo hotel. The results of the second round of voting are expected about 4.40pm AEST.

Kono has the highest numbers in public polls, but Kishida leads among lawmakers, predictions show, as senior party bosses see him more stable.

Kono is projected to obtain 39 out of 47 votes allocated to local party chapters in the runoff, public broadcaster NHK said, while Kishida is seen getting the remaining 8 votes.

A total of 429 votes are being cast in the run-off, of which 382 lawmakers and 47 local party chapters are allocated a ballot each.

The new party chief is expected to become the next prime minister as the LDP holds a majority in the parliament's powerful lower house, but the contest has created political uncertainty in Japan with four candidates.

A win by Kono or Kishida is unlikely to trigger a huge shift in policies as Japan seeks to cope with an assertive China and revive an economy hit by the pandemic, but Kono's push for renewable energy and to remove bureaucratic obstacles to reform have made him appealing to investors and business chiefs.

The next prime minister will continue with expansionary economic policy "for at least another year", as the pandemic has yet to be contained, said Ryutaro Kono, chief Japan economist at BNP Paribas.

Australian Associated Press