The plan, which will reportedly cost more than $3 billion, was first announced in August when the nations' leaders met at a summit with South Korea in Camp David outside Washington.
"In recent years, around Japan, missile-related technologies such as hypersonic weapons have improved dramatically," the defence ministry said in a statement about the agreement to jointly develop the so-called Glide Phase Interceptor (GPI).
"Strengthening interception capabilities against them is an urgent issue."
The Japanese government has already included 75 billion yen ($480 million) in its 2024 budget for development of the interceptors.
Hypersonic missiles fly at more than five times the speed of sound and have irregular trajectories, making them difficult to intercept.
The 75 billion yen is part of a record defence budget of 7.95 trillion yen approved last year, as tensions rise with China and North Korea.
Prime Minister Fumio Kishida has pledged to double defence spending to the NATO standard of two percent of GDP by 2027.
Japan has a pacifist post-war constitution, which limits its military capacity to ostensibly defensive measures.
But it updated key security and defence policies in 2022, explicitly outlining the challenge posed by China.
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