For Musashi, the answer is simple; she had not yet been commissioned. She still had several periods of testing to undergo, as well as the fitting of additional AA guns, before she was ready for service. At the time of the Battle of Midway, she was in drydock at Kure, preparing for her first speed trial, and completing the fitting of armour protection for her secondary battery.

Yamato, though, was an active part of the Japanese fleet at Midway. However, she was not part of the First Carrier Striking Force, which saw the majority of the combat during the battle. Instead, she was part of the 'Main Body' and flagship of Admiral Yamamoto, who was in overall command of the whole operation. The Main Body represented the majority of the Japanese battleship strength deployed to Midway, but saw little action as it was deployed roughly 300 miles west of the Japanese carrier force. It consisted of Yamato, the older battleships Mutsu and Nagato, the light carrier Hosho, a light cruiser and nine destroyers.

The Main Body was a key part of the Japanese strategy at Midway. The Japanese hoped that their planned landing on Midway would draw out the American fleet from its base in Pearl Harbor. The landings were to be carried out by an Invasion Force, sailing separately from the Carrier Striking Force and Main Body. The Japanese carriers would secure air superiority, and attrit the American surface forces; the battleships of the Main Body would then sweep the sea clear in a surface action. The Main Body might also be joined by part of the force sent to capture the Aleutian Islands, which would add another four battleships to the fight. To ensure that the Americans were not warned of the presence of the Japanese battleships, they had to be kept out of range of scout aircraft flying from Midway. This meant keeping them in the rear, far from the island, until it was clear that the Americans had taken the bait.

This was a complex plan, and it took little to make it go wrong. Forewarned by signals intelligence, the Americans were able to deploy before the landings on Midway were due to take place. They also did not seek to fight a surface action, as the Japanese expected. Instead, they fought the battle entirely as a carrier action, never seeking to close with the Japanese fleet. This left the Main Body out of position to help, and unable to carry out its sole purpose. During the late afternoon and evening of the 4th/5th June (depending on which side of the international date line you're in) , it did come further east. Admiral Yamamoto thought the Japanese Navy had done more damage to the American fleet than they actually had, and saw an opportunity to force a surface action. Over the course of the night, though, the risks became clearer - it was unclear how many American carriers had been sunk, and whether or not Midway's airfield had been damaged enough to make it useless. Yamamoto also discerned, through the lack of action, that the USN was moving east, making a night action impossible. Rather than risk a day action under threat from American aircraft, a recall signal was sent at 02:55 on the 5th/6th, though the Main Body would continue moving east to link up with the remnants of the First Carrier Striking Force and the Invasion Force. That evening, as the force withdrew, a single flying boat from Midway would spot the combined fleet before being chased away by fighters from the light carrier Zuiho (part of the Invasion Force). This was the closest Yamato came to action during the battle.