When the Nazis destroy Dr. Josef Mengele's (Gregory Peck) Paraguayan laboratory, Dietrich Hessen (Sky Dumont) and Arnold Schwimmer (Wolf Kahler) carry M16 assault rifles. The guns aren't used onscreen, but are presumably used to kill Mengele's Paraguayan servants and bodyguards offscreen, as we hear gunfire and see the people lying dead on the ground.
Browning Hi-Power
Dr. Josef Mengele (Gregory Peck) carries a Browning Hi-Power as his personal weapon. He uses it to kill Henry Wheelock (John Dehner) as part of his scheme to recreate the childhood of Adolf Hitler, as Wheelock's adopted son, Bobby, is (unknown to Wheelock) a clone of Hitler.
Unidentified Rifles
Henry Wheelock (John Dehner) has two lever-action rifles displayed above his fireplace mantle when Dr. Mengele comes to kill him.