Yes, the Japanese fleet included transports for an invasion force of roughly 5,000 men, split between the Imperial Japanese Army and the Imperial Japanese Navy's Special Naval Landing Forces. The invasion force was the first part of the Japanese fleet to be sighted and attacked, but was largely left unharmed. After the destruction of the Japanese carrier force, the convoy retreated, allowing the troops aboard to fight elsewhere in the Pacific. As the battle took place on both sides of the International Date Line, I will, for simplicity, be using Midway dates in this answer.

The invasion forces can be categorized into four groups. The first, and smallest, was a naval detachment tasked with capturing the islet of Kure, 60 miles west of Midway. This would allow Kure to be used as a seaplane base - to this end, the troops were carried aboard the escorts of the 'Seaplane Tender Group', one of the many sub-forces of the Japanese fleet in the battle. Midway itself would be assaulted by two separate forces. Sand Island would be assaulted by 1,500 men from the IJN's 2nd Combined SNLF. Eastern Island was to be attacked by the IJA's Ichiki Detachment (named for its commander, Colonel Ichiki Kiyonao), with 1,000 men. Once the island had been secured, two construction battalions would be landed, plus other auxiliary troops needed to establish an airfield.

Thanks to the internecine inter-service rivalries between the IJA and IJN, the two different forces departed from different ports in Japan - both forces had their own transport fleet, and they were unwilling to allow the other to use their own ships. The IJN's forces sailed from Kure, while the IJA's departed from Yokosuka. They joined together at Saipan, along with an escort under the command of Rear Admiral Tanaka Raizo. The combined force formed the Transport Group, with one light cruiser, ten destroyers, three patrol vessels, twelve transports and at least one oiler. The rest of the invasion force was made up of a support group of four heavy cruisers, which was to provide gunfire support for the landings, a minesweeping group with three minesweepers, and a main body with two battleships, a light carrier, five cruisers and eight destroyers. The invasion force would approach Midway from the south-west, hopefully drawing the American fleet towards them. This would allow the Japanese carrier force, approaching from the north-west, to surprise the American carriers from their flank.

The Transport Group (and the minesweping group) departed Saipan on the 28th May 1942, heading towards Midway as part of the general mass of Japanese ships heading that way from across the Pacific. The heavy cruisers of the support group had left Guam on the same day, while the main body had departed from Japan several days earlier. Their approach was largely uneventful. However, at 08:43 on the 3rd June, a PBY Catalina flying boat from Midway sighted the minesweeping group. At about 09:30, another PBY sighted Tanaka's transport force. At first, the PBY reported the presence of heavy Japanese units, but the true situation eventually became clear. Shortly after 12:00, a force of 9 B-17s was dispatched from Midway to attack the transport group. The bombers arrived over the transports at 16:23, acheiving near total surprise. They attacked from between 8-12,000 feet, with the Japanese unaware of their presence until the bombs began to explode. However, level-bombing against ships rarely scored hits, even at the best of times; this was no exception. Fortunately for the transports, they were out of range of Midway's more effective dive and torpedo bombers. There would be no more attacks during the rest of the day.

During the night, though, four radar-equipped PBYs, with jury-rigged torpedo-dropping equipment, were sent out to attack the convoy. One had to drop out due to bad weather, but the remaining three located the transports at about 01:30. They, again, achieved total surprise. The convoy was silhouetted against the moon, making no evasive manoeuvres, and putting up only a late anti-aircraft barrage. In the only successful American torpedo attack of the battle, one of the three PBYs scored a hit on the bow of the oiler Akebono Maru. The torpedo hit caused 23 casualties, but did only minor damage to the ship; she was able to remain in formation. At 04:30 AM on the 5th the B-17s from Midway took off for another try against Tanaka's ships. Just under an hour and a half later, though, a PBY spotted the Japanese carrier fleet, to the northwest of the island. Upon receiving this news, the American commanders at Midway directed the B-17s north to engage them. The transports would face no further attacks for the remainder of the battle. After the destruction of the Japanese carriers, they were ordered to fall back, out of range of aircraft from Midway. The four cruisers of the support group, though, would face attacks over the next few days. During the night of the 4th-5th, Mikuma and Mogami collided while taking evasive action to avoid the submarine USS Tambor. Mogami was heavily damaged, forced to slow to 12 knots. Mikuma was only lightly damaged, but was detached to protect her sister ship as she withdrew. As day broke, they were sighted by PBYs, and came under repeated air attack. Dive bombers and B-17s from Midway scored no hits. Carrier aircraft from Hornet and Enterprise, distracted by the hunt for a possible survivor from the Japanese carrier force on the 5th, arrived to attack on the morning of the 6th. Both ships suffered multiple hits. Mikuma was set ablaze and abandoned, while Mogami, thanks to well-executed damage control, survived, albeit with heavy damage.

After the battle, the Japanese troops were largely sent to the South Pacific. The 2nd Combined SNLF was split into its two constituent units, the 5th Kure and 5th Yokosuka SNLF. Both would see service in New Guinea, with some elements of the 5th Yokosuka SNLF also being committed to Guadalcanal. The Ichiki Detachment was one of the first IJA units to be sent to Guadalcanal. There, they would be wiped out, following a frontal assault against dug-in USMC positions along the Tenaru river.