This distinction is mainly due to the nature of their combat roles. IJN sailors and officers were usually confined to their ships and naval installations while the army had closer contact with civilians and guerrillas in China, Korea and Indochina. The Japanese Navy, aside from finding stranded US pilots and sailors, had less contact with prisoners (hence fewer war crimes). After the strategic defeat at Midway and subsequent setbacks the Navy was put on the defensive and confined to resupplying islands in the Pacific while trying to slow down the US advance westward.

What contact they had with US forces indicates that the Japanese Navy was no less restrained or more "honorable" than the army. Following the Battle of Midway several American pilots were picked up by the IJN. Two were interrogated then bound in rope, attached to weighted fuel drums and thrown off the destroyer that picked them up. Another was thrown off the Japanese destroyer Arashi and managed to cling onto chains on his way down but was summarily dispatched with a fire ax. Obviously these sailors would have been pissed off after losing four aircraft carriers at Midway, but as with the Japanese army in China the brutality was systematic, not just incidental. Beginning in 1943 Japanese submarines were ordered to kill all survivors of the merchant ships they sank. When the SS Jean Nicolet was torpedoed in the Indian Ocean a Japanese submarine surfaced to pick up 60 survivors, who were then beaten, stabbed and thrown to sharks by the crew. Besides routinely killing survivors of torpedoed merchant ships, the IJN strafed lifeboats or enemy combatants they found in the water.

The Japanese Army and Navy during WW2 were certainly distinct subcultures that often disagreed and failed to cooperate effectively but they prosecuted the war in the same way. Japanese soldiers singled out US medics on the battlefield to kill both them and the men they could potentially save. Similarly, the Australian hospital ship Centaur was torpedoed despite being brightly illuminated and painted in full white with huge red crosses. Both the Army and Navy aimed to inflict maximum casualties and fear on the Americans. Both were animated by the same mindset composed of a belief in a semi-divine emperor and Japanese racial superiority combined with the frustration of having these two beliefs challenged while fighting a losing war.

Sources: http://www.pacificwar.org.au/JapWarCrimes/TenWarCrimes/WarCrimes_Jap_Navy.html Inventing Japan Ian Buruma The Rising Sun: The Decline and Fall of the Japanese Empire John Toland