The naval exercise featured 95 aircraft, 16 ships and two submarines, officials said in a statement.
Various maneuveres were undertaken in rough seas in the Bay of Bengal, they said.
The exercise, which began on July 10, comprised both on shore and offshore activities which included cross deck flying operations, refuelling across ships and crew handling procedures.
Under cross deck flying operations, a helicopter from USS 'Shoup' landed on-board Indian Naval Ship 'Sahayadri' and later on Japanese Naval ship 'Sazanami', the officials said.
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"The cross deck flying operations require a high degree of interoperability and knowledge of procedures of participating in ships and helicopters", they said.
The navies of the three countries undertook the exercise in rough seas and under challenging weather conditions.
Under the crew exchange programme, an Indian Navy helicopter transferred Japanese sailors to Naval ship Vikramaditya in the Bay of Bengal. This was followed by flying operations by helicopters of US Navy ships.
Yesterday, Indian Navy ship Jyoti transferred oil with US 'Shoup' and Japanese naval ship 'Sazanami' under the replenishment at sea exercise.
On combined crew training exercise, MiG 29K fighter air craft from INS Vikramaditya undertook combat missions against US Navy F-18 fighter aircraft launched from USS Nimitz.
Aircraft from both Indian and US Navies undertook composite formation flying, demonstrating another step in the interoperability aimed through this exercise, the statement added.