The girl, who has not been convicted on any offence, is being housed in a cell in a special annexe of the prison inside the perimeter wall.
She is kept away from adult inmates but can mix with offenders aged up to 16.
She has been at the jail for four days on remand and will go before the court again on Wednesday where she could be sentenced to return to the prison. Until a few days ago a 14-year-old was also at the jail awaiting trial, but has been released after his parents agreed to take care of him.
A civil liberty group pledged yesterday to take the case to the United Nations Committee on the Rights of the Child.
The juveniles at Victoria Road Prison in Douglas, the island's capital, are locked in modern, adult-style cells from about 8pm to 8am.
Under island laws, children as young as 10 can be detained in the island's only prison, which currently holds three youths aged under 17, two female adults and 88 male inmates.
The 12-year-old girl was sent to the prison last Wednesday. It is understood she is accused of assaulting social workers and damaging property.
The 15-year-old boy at the jail is understood to be serving a six- month sentence for assault and theft.
In the United Kingdom, child offenders aged under 15 are kept in local authority secure accommodation. Penal experts have warned of the dangers of mixing different age groups and sexes and of keeping children in prisons.
Terence McDonald, a Manx advocate, called yesterday for the island's government to establish separate secure accommodation for child criminals. "It is barbaric to lock up children in jail and place them in cells," he said.
"We are rich society and should have a proper accommodation."
Bernard Moffatt, secretary of the Manx Council for Civil Liberty, said his organisation would appeal to the UN: "Locking children up in adult prisons is like something from the Dark Ages. It has got to end."
The Isle of Man has a reputation for retaining harsh, archaic laws. Homosexuality was illegal until 1992 and hanging was only abolished in 1993. In the same year the government voted to retain birching.
There are five cells in the juveniles unit, which have toilets and basins. They are sometimes used by adults when the unit is empty. Parents are allowed to visit every day and the children receive education and recreation. The prison staff who supervise them are given special training.
Rosemary Crosby, the jail's governor, said: "There is a need to put some children in secure accommodation. It is how you deal with them when they are there that is important. We do not have the resources to provide greater facilities."