In addition to aerial reconnaissance, two picket lines of submarines would be positioned across the presumed line of advance of the Americans. The southern cordon ("A"), and northern cordon ("B"), were each composed of seven fleet boats. However, the submarines of both groups were assigned fixed positions, rather than being placed in patrol boxes in which they could operate freely. Worse, the patrol lines did not have overlapping fields of vision, making them porous indeed. This static mode of employment (which was typical of Japanese submarine operations throughout the war) meant that the big Imperial Navy boats could not be concentrated on enemy units with anything like the flexibility that the Germans were currently employing in the Atlantic.
…an omniscient observer would also have noticed that by this time the Japanese strategic scouting plan for Operation MI had fallen completely to pieces. The submarine cordon lines, upon which Nagumo was counting for early warning of northward-advancing Americans, were tardy in taking their positions, having left Kwajalein late. But even had they left on time they would have missed the American carriers. By the time Cordon A and B were established, the Americans had already slipped past it.
The reasons for the failure of the submarine picket lines, which were not properly understood until after the war, verge on the scandalous. The commander of Sixth Fleet, Japan's submarine forces, was Vice Admiral Marquis Komatsu Teruhisa, the cousin of the empress of Japan, and a close personal friend of Emperor Hirohito. The marquis was a great fan of Yamamoto's and had such confidence in the Midway operation that in his opinion the battle was as good as won. So much so, in fact, that he was already preoccupied with follow-up plans to attack the Panama Canal and terrorize California. He thus paid little attention to the nuts and bolts of the deployment against Midway. While he was supposed to be at the staff planning sessions held on board Yamato, Komatsu did not attend, sending his staff instead. Furthermore, according to Gordon Prange, the submarine cordon details "never appeared in the official orders for Operation MI. Writing up the submarine portion of such orders was a normal responsibility of Commander Arima Takayasu, Yamamoto's submarine officer. But for some reason, Captain Kuroshima told Arima that he had no need to do so." This rather incredible oversight meant that the Japanese boats were committed to action without a workable operational plan.
Furthermore, the boats that were tasked for the operation-the older vessels of SubRon 5-were far from ideal for the mission. None of them could dive safely past 200 feet, and all of them were under refit during the April-May period, with the intent of being shordy moved into the reserve fleet and relegated to training purposes. Not surprisingly, Commander Iura Shojiro of Naval GHQ's submarine staff protested to Admiral Fukudome that the boats were too slow and balky to get on station in a timely manner, nor could they cope with air attacks and patrols once they got there. His protests fell on deaf ears.
As matters developed, Iura was completely correct in his estimation of SubRon 5's weaknesses. Their overhauls took too long, and the boats were late in leaving Kwajalein, departing between 26 and 30 May. Worse yet, the long daylight hours, coupled with intensifying American patrol activity, meant that the boats had only limited time during the night to transit on the surface. During the days they were often forced to dive to avoid Catalinas, creeping forward submerged as best they could. The result was that while the boats were scheduled to be in place by 1 June (local), some of them didn't reach their stations until 3 June, by which time the American carriers had already passed through." Had the American task forces been sighted in the vicinity, Yamamoto and Nagumo would have had both actionable information and the time to make last-minute adjustments to their operational plans. As it was, they received neither.
It would appear that because of Komatsu's membership in the imperial family, he was never held to account for this crucial failure. As one observer later noted, "Japanese historians in later years would allude to [the event] only obliquely, and American historians . . . would [necessarily] follow the lead of the Japanese." One example of such an oblique reference is supplied by Admiral Ugaki, who remarked after the battle in his diary that "we failed to make good use of subs in reconnaissance," despite having ordered the cordons in place to prevent the very sort of ambush that in fact occurred.