Following filming of a flying stunt on M40 motorway in Buckinghamshire (which was newly completed but not yet open to traffic) Joan Hughes (pilot of the Tiger Moth) was charged but later acquitted of seven counts of dangerous flying when the 'plane failed to make contact with the surface of the while passing under a bridge. A crosswind had prevented Hughes from landing the plane on the road before passing under the bridge as stipulated as a condition of permission to use the location. Norman Foster (who supervised the shooting of this scene) was also charged but acquitted of three counts of aiding and abetting. In addition to the court case filming permission was revoked immediately, leading to the sequence being completed with a miniature set of the site and the model aircraft used for other flying sequences.
Production on this film began after Gerry Anderson began work on Captain Scarlet and the Mysterons (1967), a series that used far more realistic-looking Supermarionation puppets. Anderson reportedly considered making Thunderbird Six in the same style, but decided for reasons of continuity to retain the big-head style of puppets for the film. Apparently, some of the new style puppets are visible in some scenes.
The puppet of Cliff Richard (used in the film Thunderbirds Are GO (1966) makes a cameo appearance, disguised with thick-rimmed glasses and a mustache, sitting behind Lady Penelope at the Whistle Stop Inn.
During the evacuation of the missile base, one of the cars driving through shot is Sam Loover's car from Joe 90. Footage of the destruction of the missile base also appears in the opening episode of Joe 90.
At one point in the film, Virgil says, "I've got a tiger in my tank." This was the slogan of an ESSO advertising campaign in the UK ("Put A Tiger In Your Tank") at the time the film was being scripted.
The Thunderbirds puppets are famous for their disproportionate appearance in both the TV series and the first film (Thunderbirds Are GO (1966)). For this, their final outing, the puppets were redesigned with closer to normal proportions.
The scene with FAB1 and Alan and Tin Tin skiing was made on the largest set ever constructed for Thunderbirds, around 50 feet long, with the car and skiers was only 1 inch high. The "snow" was made from salt.
In the first scene when all the men in the meeting room are laughing (which is the only time in any of Gerry Anderson's puppet series that this happens), you can see fillings in the teeth of one of the puppets.