[3] Three demilitarized F-104A airframes with an additional 6,000 lbf (27 kN) Rocketdyne LR121/AR-2-NA-1 rocket engine and modified systems, used for astronaut training at altitudes up to 120,800 ft (36,820 m).

[2] Dual-control trainer version of F-104J for Japanese Air Self-Defense Force, 20 built by Lockheed and assembled by Mitsubishi.

Manufactured by Lockheed, and under license by Canadair and a consortium of European companies which included Messerschmitt/MBB, Dornier, Fiat, Fokker and SABCA.

Upgraded avionics included a new Autonetics NASARR F15A-41B radar with air-to-air and ground mapping modes, the Litton LN-3 Inertial Navigation System (the first on a production fighter) and an infrared sight.

One aircraft used by Lockheed as a demonstrator with the civil registration number L104L, was flown by Jackie Cochran to set three women's world speed records in 1964.

Specialized interceptor version of the F-104G for the Japanese ASDF, built under license by Mitsubishi for the air-superiority fighter role, armed with cannon and four Sidewinders; no strike capability.

Produced mainly by Fiat and Aeritalia (one aircraft was lost before delivery), upgraded for the interception role having NASARR R-21G/H radar with moving target indicator and continuous wave illuminator for SARH missiles (initially AIM-7 Sparrow), two additional wing and two underbelly hardpoints (to give a total of nine), uprated J79-GE-19 engine with 52.8 kN (11,870 lbf) thrust (79.6 kN/17,900 lbf with afterburner), and two additional ventral fins for increased stability at high Mach numbers.

[4] Aircraft allocated to air defence missions had their 20 mm (.79 in) M-61 Vulcan cannon removed.

[4] (Aggiornamento Sistemi d'Arma – "Weapon Systems Update") – An upgraded F-104S, 147 were modified from existing airframes, with Fiat R21G/M1 radar with frequency hopping, look-down/shoot-down capability, new IFF and weapons delivery computer, and provision for AIM-9L all-aspect Sidewinder and Selenia Aspide missiles.

[2] (Aggiornamento Sistemi d'Arma/Modificato – "Weapon Systems Update/Modified") – 49 F-104S-ASA and 15 two-seat TF-104G aircraft upgraded from 1998 to ASA/M standard with GPS, new TACAN and Litton LN-30A2 INS, refurbished airframe, and improved cockpit displays.

200 Canadian-built versions, built under license by Canadair[2] and optimized for both nuclear strike and 2-stage-to-orbit payload delivery, having NASARR R-24A radar with air-to-air modes, cannon deleted (restored after 1972), additional internal fuel cell, and Canadian J79-OEL-7 engines with 10,000 lbf (44 kN)/15,800 lbf (70 kN) thrust.