Wahoo was ready for sea again on 16 January 1943. She performed sonar tests in Moreton Bay with USS Patterson (DD-392) before beginning her third war patrol. Three days later, the submarine passed into Vitiaz Strait en route to her patrol area. Wahoo's orders were to reconnoiter Wewak, a Japanese supply base on the north coast of New Guinea between Kairiru Island and coincidently, Mushu Island. There was one large problem: Wahoo had no charts of the harbor. However, it turned out that motor machinist's mate Dalton Keeter had bought a cheap school atlas while in Australia. It had a map of New Guinea with a small indentation labeled "Wewak". With that as a reference, a blowup of the Navy chart was made.
Japanese destroyer Harusame torpedoed by Wahoo.On 24 January 1943, Wahoo dove two miles (3 km) north of Kairiru Island and proceeded around the western end to penetrate Victoria Bay. She sighted the Japanese destroyer Harusame with RO-class submarines nested around it. The destroyer was getting underway, so Wahoo fired a spread of three torpedoes at the moving target; all missed aft. Another torpedo was fired, but the destroyer avoided by turning away, then circled and headed for Wahoo. Wahoo turned toward the destroyer and at a distance of 750 yards (690 m) fired one last torpedo. This torpedo struck the destroyer amidships, breaking its back. Wahoo had no difficulty escaping the area. Despite heavy damage Harusame was beached and repaired.
The next day, Wahoo changed course for Palau. On 26 January, the submarine sighted the smoke of two ships. Wahoo obtained a position, launched two torpedoes at the leading ship and, 17 seconds later, two at the second ship. The first two torpedoes hit the Fukuei Maru. The third passed ahead of the second freighter, the fourth hit. Upon observing the damage, Wahoo discovered there were two more ships; a huge transport, the Buyo Maru, and a tanker. The Fukuei Maru was listing badly to starboard and sinking by the stern; the second ship was headed directly for Wahoo, at a slow speed. Ignoring this, Wahoo fired a three-torpedo spread at the transport; the second and third hit and stopped her.
Turning her attention to the second target, which was still headed for her, Wahoo fired two bow tubes "down the throat" to stop him. The second torpedo hit, but the target kept coming and forced the submarine to turn hard left at full speed to avoid being rammed. There followed so many explosions that it was hard to tell what was happening. Returning to periscope depth, Wahoo observed the Fukuei Maru had sunk; the second target was still moving, evidently with steering trouble; and the transport, Buyo Maru, was stopped but still afloat.
Wahoo headed for the transport and fired a bow tube; the torpedo passed directly under the middle of the ship but failed to explode. The sub then fired another torpedo which headed right for the stack and blew the target apart midships. The submarine then headed for the crippled freighter, which had formed up with a tanker, and both ships were moving away. Wahoo decided to let these two ships get over the horizon, while she surfaced to charge her batteries and attack the shipwrecked Japanese now sitting in about twenty lifeboats. Controversy still attaches to this action in that troops in the water may have been deliberately targeted by Wahoo. Vice Admiral Charles A. Lockwood, the contemporary COMSUBPAC, asserts that the survivors were army troops and turned machinegun and rifle fire on Wahoo while she maneuvered on the surface, and that such resistance was common in submarine warfare. Richard O'Kane stated that the fire from Wahoo was intended to force the troops to abandon their boats and that no troops were deliberately targeted. Clay Blair, states that Morton opened fire first and the shipwrecked returned fire with handguns.
After some time, Wahoo moved away to intercept the two fleeing ships. She decided to attack the tanker first since she was as yet undamaged. With only four torpedoes left, the submarine fired two at the tanker, the second hitting her just abaft of midships, breaking her back; she went down almost instantly. Wahoo then turned her attention to the freighter and fired her last two torpedoes without a spread. They both hit. Fifteen minutes later, the freighter sank, having absorbed four hits from three separate attacks. Wahoo then set a course for Fais Island. Postwar, JANAC credited Wahoo with only three sinkings: the transport, Buyo Maru (5,300 tons), Fukuei Maru (2,000 tons), and an unknown maru (4,000 tons).
A broom on the USS Wahoo, Pearl Harbor, 1943On 27 January 1943, Wahoo made contact with a convoy of eight ships, including two freighters and a tanker. Efforts to gain a position were foiled by a persistent destroyer escort who dropped six depth charges. The submarine had no option but to retreat since she had previously expended all torpedoes. The next day, Wahoo sighted Fais Island, and her plan to shell a phosphorite refinery was scrapped due to the untimely appearance of an inter-island steamer.
The submarine left station and arrived at Pearl Harbor on 7 February, only 23 days after leaving Brisbane (most patrols were in the 60?75 day range). Prior to entering the naval base, Wahoo donned topside embellishments to celebrate her victory. A straw broom was lashed to her periscope shears to indicate a clean sweep. From the signal halyard fluttered eight tiny Japanese flags, one for each Japanese ship believed to have been sunk by Wahoo to that point in the war.
Wahoo commenced refit by a tender relief crew and the ship's crew. On 15 February, refit was completed, and the submarine was declared ready for sea on 17 February. She then conducted two days of training and was drydocked at the Submarine Base, Pearl Harbor, on 21 February.