The P6M-2 was an impressive aircraft; its Mach 0.9 (1,100 km/h) performance "on the deck" could be equaled by few aircraft of the time. The aircraft were heavily built, with the skin at the wing roots over 1 in (25 mm) thick. The normally docile and pleasant handling characteristics of the P6M-1 were replaced by some severe compressibility effects above Mach 0.8. These included rapid changes in directional trim, severe buffeting, and wing drop requiring high control inputs to counter. Until those problems were fixed, the P6M-2 could not be considered for use by the Fleet.
The problems were identified as being caused by the larger engine nacelles required for the J75s. There were also problems on the water, including a tendency for the tip floats to dig in under certain situations, and engine surges. These problems were eventually solved, but time had run out just as the first crews were training for its operational debut. Eisenhower's administration was making major defense budget cuts that forced the Navy to make choices.
In August 1959 Martin was told to halt operations and the program was about to be canceled. Seaplanes were a small community in Naval Aviation, and the P6M was significantly over budget and behind schedule and competing with aircraft carriers for funding. The Navy also had a potentially superior system for the nuclear strike role, the Ballistic Missile Submarine.
Martin tried unsuccessfully to market the technology in the civilian market, with a version called the SeaMistress but there were no takers, and the company soon abandoned the aircraft business entirely to focus on missiles and electronics. The P6M was the final aircraft constructed by the Glenn L. Martin Company. A literal swan song aircraft for its company.