In other allegations heard by the inquiry, one Iraqi said he had his face burnt when it was held next to a generator, a man was forced to lie face-down over a hole in the ground filled with excrement, and the detainees were "continually beaten" for hours on end.
Gerard Elias QC, counsel to the inquiry, said: "There can be little doubt that the detainees, or some of them, were the targets of physical assaults.
"They were beaten more or less continuously over the 48-hour period, kicked and punched a very large number of times, especially in the kidneys and lower back."
The inquiry also heard allegations that soldiers tried to manipulate detainees' moans into an "orchestrated choir".
Mr Elias said: "There was shouting, moaning - even screaming - coming from the TDF (temporary detention facility) from time to time during the detention, according to some witnesses.
"And the inquiry will hear scandalous accounts of an orchestrated choir of victims' reactions."
The opening statement by Mr Elias is expected to take two weeks, and the entire inquiry about a year.
It will be divided into four modules which will examine:
• The history of "conditioning" techniques, like hooding, used by UK troops while questioning prisoners from Northern Ireland in the early 1970s to the invasion of Iraq in March 2003
• What happened to Mr Mousa and other Iraqi detainees
• Training and the chain of command
• Events since 2003 and any recommendations for the future
Mr Mousa was arrested at the Haitham Hotel in Basra, where he worked as a receptionist, on 14 September 2003.
British soldiers looking for weapons found assault rifles, pistols and suspected bomb-making equipment.
Hotel staff insisted the weapons were used for security but Mr Mousa and nine other Iraqi civilians were taken to a detention centre under suspicion of being insurgents.
By Peter Jackson, BBC News
One of the key issues the inquiry will explore is why five "conditioning" techniques inflicted on IRA suspects in 1971 - then later banned - were used on the Iraqi detainees.
The interrogation tactics of hooding, stress positions, sleep deprivation, food and water deprivation, and white noise were outlawed in 1972 by then prime minister Edward Heath.
A report at the time, led by Edmund Compton, controversially found the techniques constituted physical ill-treatment but not torture.
Gerard Elias QC told the Baha Mousa inquiry that in Iraq neither frontline soldiers nor those higher up the chain of command seemed to know their obligations under international law.
Even after Mr Mousa's death, the army was unclear whether the ban applied outside Northern Ireland, he said.
As this inquiry explores the treatment of Mr Mousa and the other Iraqis - and the training and orders given to those involved in their detention - it will bring to light what lessons, if any, were learned from the 1970s.
Two days later Mr Mousa was dead. A post-mortem examination showed he suffered asphyxiation and had at least 93 injuries to his body, including fractured ribs and a broken nose.
After an initial investigation by the Royal Military Police, a six-month court martial followed with seven soldiers facing war crimes charges relating to Mr Mousa's death.
In April 2007, all but one were cleared on all counts at Bulford Camp in Wiltshire, but Cpl Donald Payne, 36, was jailed for a year and dismissed from the Army.
He also became the UK's first convicted war criminal under the International Criminal Court Act.
The court martial revealed confusion among military officers about whether "conditioning" techniques - the "softening up" of prisoners before interrogation - were lawful or not.
Methods can include hooding, depriving detainees of sleep, as well as making them stand with knees bent and hands outstretched.
Prosecutors told the court martial the techniques were banned under the Geneva Convention but soldiers said they were common practice within some military units in Basra in 2003.
In July last year the MoD agreed to pay £2.83m in compensation to the families of Mr Mousa and the nine other men detained with him.
Attorney General Baroness Scotland has ruled that any soldiers giving evidence to the inquiry will be immune from disciplinary action even if it suggests they have lied or withheld information previously.
Their own testimony also cannot be used to decide whether to prosecute them but evidence from other witnesses could still lead to criminal proceedings.
Nearly all British troops were withdrawn from Iraq this summer.
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