Shooting on the movie was wrapped up early by studio executives, in the interest of controlling costs, before some important scenes were filmed. Charlton Heston offered to return his entire salary for the movie if the studio would agree to film the opening scene - the massacre of soldiers and civilians by the Apaches - and some re-shoots. The studio kept his paycheck and never allowed any more footage to be shot anyway.
During the filming of this movie, Sam Peckinpah was so obnoxious and abusive towards his actors that Charlton Heston physically threatened the director with a sabre. Heston later remarked that this was the only time he had ever threatened anybody on a movie set.
Woody Strode was considered for the part that went to Brock Peters. Strode was part Native American and he wrote in his memoirs that he didn't get the part because he was told by Sam Peckinpah that he looked too much "like a half-breed" to play the part.
After the success of Sam Peckinpah's later The Wild Bunch (1969), Columbia told him that they would allow him to re-shoot parts of this film that had been cut from the released version. Peckinpah, naturally, declined the offer.
According to both Paul Seydor's book "Peckinpah: The Western Films, A Reconsideration" and David Weddle's book "If They Move, Kill 'Em", this film was originally budgeted at $4.5 million and scheduled for 75 days of principal photography, which was appropriate for a road-show release. But only two days before Sam Peckinpah, his cast and crew were to start filming in Mexico, a change in the top brass at Columbia occurred, and the new regime cut the budget down by $1.5 million, and the schedule down by 15 days, making it a standard western release. As could be expected, Peckinpah considered this an act of extreme betrayal.
Sam Peckinpah had been pitching a movie about Lieutenant Colonel George Armstrong Custer and the Battle of the Little Big Horn, because he thought it was fascinating how Custer became a glorious, immortal American hero after being defeated in battle and killed. Nothing ever came of it, but Peckinpah thought the story of "Major Dundee" to be similar enough, and took this job instead.
Despite his quarrel with Sam Peckinpah, producer Jerry Bresler fought very hard with Columbia to keep the 136-minute cut (the "Extended Edition" now on DVD) despite its poor reception at its preview, but was rebuffed by the studio.
Tyreen's quote, on finding Dundee in Durango, 'Awake for Morning in the bowl of night has cast the stone that puts the stars to flight ...' , is from the 'The Rubaiyat of Omar Khayyam', translated by Edward Fitzgerald
Sam Peckinpah originally wanted Lucien Ballard, with whom he had had a good working relationship on Ride the High Country (1962), as the director of photography, but producer Jerry Bresler refused the request, making him work with Sam Leavitt, whose credits included Diamond Head (1963), a previous Bresler production, and Cape Fear (1962). Although Leavitt did get along fairly well with Peckinpah, this was the first sign of tension between the director and the producer.