1 September 1941, Yura was appointed flagship of Rear Admiral Daigo Tadashige's Submarine Squadron 5 and was based in Hainan. At the time of the attack on Pearl Harbor, Yura was covering the first wave of the Malaya Invasion Force south of the Cape of Camau, French Indochina. On 9 December 1941, Yura and her squadron were ordered to pursue and sink the Royal Navy "Force Z" (the battleship , battlecruiser and supporting destroyers). Although Yura received word from the submarine that the British ships were spotted, due to poor wireless reception, the location was unclear and the British vessels were overwhelmed by torpedo bombers of the IJN 22nd Air Flotilla from bases in Indochina before Yura and her submarines could take action. Yura was then assigned to the invasion of Sarawak from 13 – 26 December 1941, covering landings in Brunei, Miri, Seria, and Kuching. The 2,500 men of the "Kawaguchi Detachment" and the No. 2 Yokosuka Special Naval Landing Force (SNLF) quickly captured Miri's airfield and oil fields. The operation was completed, and Yura returned to its base at Camranh Bay, Indochina by the end of the year. In February, Yura was assigned to Vice Admiral Ibō Takahashi's IJN Third Fleet, to cover the invasion of Sumatra, protecting the landings of troops at Palembang, Banka Island, and Bantam Bay and Merak on Java. On 1 March 1942, the Dutch submarine made visual contact with Yura and attacked, launching two torpedoes from 2500–3000 meters, but both either missed or were duds. The Japanese made six depth charge attacks, dropping about 25 depth charges, but K XIV survived and escaped via Sunda Strait to Colombo, Ceylon. On 4 March, Yura rescued the crew of the tanker Erimo (sunk by the submarine ). On 6 March, Yura was assigned to the No. 1 Escort Unit, and continued to cover troop landings in Sumatra and the Andaman Islands through the end of the month. Indian Ocean Raids In April, Yura was assigned to the raids in the Indian Ocean under Vice Admiral Jisaburō Ozawa's Second Expeditionary Fleet. Yura, accompanied by the destroyers , , , and , departed Mergui and steamed into the Bay of Bengal with the cruisers and , , and and the light carrier to attack Allied merchant shipping. On 6 April 1942, east of Kalingapatnam in the Bay of Bengal Yura and Yūgiri sank the Dutch merchant vessel