A spokesman for the U.S. attorney’s office for the Southern District of New York, which opposed Dr. Kanayama’s effort to stop his extradition, declined to comment on the ruling. But federal prosecutors said in court papers that Dr. Kanayama had agreed to surrender to the U.S. Marshals Service on Monday and to be transferred to Japanese custody the next day. They had characterized his petition as a “last-minute gambit to avoid extradition.”