In 1937, in response to increasing demands from the Japanese military for resources from the Japanese merchant fleet, Murata organized an Autonomous Shipping Control Group (海運自治連盟, Kaiun Jichi Renmei), of which he served as chairman, to reduce competition and coordinate efforts between the seven largest shipping companies and the government.

Murata was representative of successful private entrepreneurs who were invited to join the Taisei Yokusankai political organization created by Fumimaro Konoe and his followers, and took active participation in debate on the state socialist controlled economy created under the National Mobilization Law.

As ambassador he brought a team of scholars from Japan to make a research report with recommendations for the collaborationist government, told President José Laurel that the Philippines had the right to make more demands upon the Japanese government; however, his report and efforts were ignored by the Japanese military.

In 1946, along with all members of the wartime Japanese government, Murata was purged from public office and was taken into custody by the American occupation authorities and held at Sugamo Prison, where he was to be charged for war crimes.

He also appointed special ambassador to the Philippines in 1954, and worked towards normalization of relations and settlement of war-time compensation claims.