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Suga received 377 votes in the election to pick a successor to Prime Minister Shinzo Abe, reports AP.
The other two contenders former Defense Minister Shigeru Ishiba and former Foreign Minister Fumio Kishida received a combined 157 votes.
Abe announced last month that he would resign on health grounds.
Read Also: Japan PM Shinzo Abe resigns for health reasons
The expected victory in the party vote by Suga, the current chief Cabinet secretary, all but guarantees his election in a parliamentary vote Wednesday because of the majority held by the Liberal Democrats’ ruling coalition.
Despite his low-key image as Abe's right-hand man, Suga is known for his iron-fist approach to getting jobs done as a policy coordinator and influencing bureaucrats by using the centralised power of the prime minister's office.
Suga says that he is a reformist and that he has worked to achieve policies by breaking territorial barriers of bureaucracy. He has credited himself for those efforts in achieving a booming foreign tourism industry in Japan, lowering cellphone bills and bolstering agricultural exports.
Compared to his political skills at home, Suga has hardly traveled overseas, and his diplomatic skills are unknown.
In addition to the coronavirus and the economic fallout, Suga stands to inherit several other challenges, including China, which continues its assertive actions in the East China Sea.
He also will have to decide what to do with the Tokyo Olympics, which were pushed back to next summer due to the coronavirus. And he will have to establish a good relationship with whoever wins the US presidential race.