A commando who admitted taking part in one of the rituals while in Britain claimed that the practice, known as "japping", was common at his elite unit's home base and on missions abroad. Gnr Timothy Lyons, with the 29 Commando Regiment, said that the ceremonies were seen as "fun" and an accepted part of military life.
Referring to incidents in Iraq in the aftermath of the US-led invasion in 2003, he said: "When somebody was leaving a battery in Iraq, there were two containers saved up which were full of excrement and urine. They were tied up and those were thrown over them in the desert."
The allegations will make uncomfortable reading for military commanders who are already smarting at adverse publicity caused by the alleged mistreatment of Iraqi prisoners by troops in Basra, southern Iraq. A separate court martial is being heard in Germany.
Lyons, 21, who has no connection with the proceedings in Germany and whose Royal Artillery unit is attached to the Royal Marines, was facing charges of assault and battery on a colleague while at the unit's base in Plymouth.
The court martial was told that Lyons attacked Gnr Neil Piper in July 2003 while taking part in a japping, attended by more than 20 soldiers, where the victim was tied to an ironing board and had a BB gun - a low- powered air gun - fired at him. He was also alleged to have been indecently assaulted with a broom handle.
Col Nigel Jones, for the prosecution, said the ceremony reinforced a "them and us" culture dictated by which soldiers had undergone the Marines' rigorous commando training.
Asking why Gnr Piper had been singled out, Col Jones said: "It could be because he was NCT [non-commando trained]. NCTs were known as `crap hats', weren't they? It's a derogatory term. He was an NCT and he was a bit gobby. That was why he had been picked, wasn't it?"
Lyons admitted he used his BB gun to shoot at Gnr Piper but insisted his comrade had taken it as a joke.
Lyons, who with two other colleagues had admitted charges of battery and common assault, was cleared by a three-man panel of causing actual bodily harm by pushing his victim while still attached to the ironing board, causing bruising and a suspected broken cheek bone. He will be sentenced next week.