Meeting in Japan on July 28, they will discuss "security challenges facing the two countries" and the "strengthening of the deterrence and response capabilities of the Japan-US alliance", a ministry statement said.
It follows a state visit by Japan's Prime Minister Fumio Kishida to Washington in April.
At that meeting, Kishida and President Joe Biden unveiled plans to restructure the US military command in Japan, the biggest such change since the 1960s.
The move was aimed at making US and Japanese forces more nimble in the event of threats, such as a Chinese invasion of Taiwan.
Blinken and Austin will also hold a "ministerial meeting on extended deterrence" when they meet Japanese Foreign Minister Yoko Kamikawa and Defence Minister Minoru Kihara, Monday's statement said.
"The four Ministers will discuss bilateral cooperation to further strengthen US extended deterrence, bolstered by Japan's defense capabilities," it said.
Japan plans to double its defence spending to the NATO standard of two percent of GDP by 2027, although the falling value of the yen may dent its purchasing power.
Blinken will be in Japan from July 28-29 as part of a trip that also includes an Association of Southeast Asian Nations (ASEAN) ministerial meeting in Laos this week.
He said on Friday he would meet his Chinese counterpart Wang Yi on the sidelines of the ASEAN meeting.
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