Later, it was used as a scout for the Attack on Pearl Harbor, and it was encountered in combat by the United States Navy during the Battles of Coral Sea and Midway.

One example (MSN 4326) was surrendered to New Zealand forces after the end of hostilities, and it was flown briefly by RNZAF personnel, but not repaired after a float was damaged, and subsequently sank at its moorings in Jacquinot Bay.

[4] Trainer version with dual controls Redesigned floats, improved radio equipment Night-flying conversion As E13A1a, with Air-Surface radar Night-flying conversion of above Anti-surface vessel version equipped with two downward-firing belly-mounted 20 mm Type 99 Mark II cannons in addition to bombs or depth charges The wrecks of a number of sunken aircraft are recorded.

The wreckage of one aircraft is located on-land at an abandoned seaplane base at Lenger Island, off Pohnpei in the Federated States of Micronesia.

[9] Another Aichi, a model E13A1 (MSN 4116) was raised from the sea in 1992, close to Minamisatsuma (called Kaseda at the time), and is now on display at the Bansei Tokkō Peace Museum.