The announcement came a day after Pyongyang conducted its third test launch of its Hwasong-18 intercontinental ballistic missile, the largest weapon in its arsenal.
"The full operational capability of the real-time sharing system for North Korean missile warning data was confirmed through a recent pre-evaluation and is currently in normal operation," the ministry said in a statement.
"The three countries established the system to ensure the safety of its citizens... by detecting and evaluating missiles launched by North Korea in real time," it added.
The data-sharing system was part of an agreement between the defence chiefs of the three countries last month, which also included setting up multi-year plans for trilateral military exercises.
The ministers were following up on agreements reached by their leaders at a three-way summit hosted by US President Joe Biden at Camp David in August.
North Korean leader Kim Jong Un, who personally oversaw the latest launch, said it demonstrated options that Pyongyang would take "when Washington makes the wrong decision".
Seoul and Washington have ramped up defence cooperation in the face of a record-breaking series of weapons tests by Pyongyang this year.
South Korea's conservative government of President Yoon Suk Yeol has also made a concerted effort to improve historically strained ties with Japan, the country's former colonial ruler.
The Camp David meeting marked the first time the three leaders had met for a standalone summit, rather than on the sidelines of a larger event.
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