Hundreds of migrant workers who have had documents seized by employers are being held for months in deportation centre

The "widespread" practice of confiscating low-income workers' passports in Qatar has left hundreds languishing for up to a year in the Gulf state's deportation centre, the Guardian has learned.

Amnesty International has uncovered evidence linking the Qatari government to the practice. Some employers gave domestic workers' passports to authorities at the interior ministry if workers absconded, the human rights group discovered. "This practice suggests that the government may implicitly accept the principle that domestic workers do not hold their own passports," says an Amnesty report, "My Sleep Is My Break": Exploitation of Migrant Domestic Workers in Qatar, published on Wednesday.

All of the dozens of domestic workers the Guardian met in Qatar during an investigation in January had been forced to hand over their passports to employers. François Crépeau, the UN special rapporteur on the human rights of migrants, met just one worker who had managed to retain his passport when he visited the Gulf state in November.

The man was in the overcrowded deportation centre in which more than 1,300 people were detained. Visitors to the female quarters of the building on the outskirts of the capital, Doha, have described seeing babies and up to three women sleeping on a single mattress.

"[In] the wards we visited, there were simply too many people for the space there was," said Crépeau, who will present a report on his Qatar findings to the UN in June.

The use of mobile phones is forbidden in the deportation centre and officials told Crépeau this was for security reasons. There is telephone access, but detainees complained the lines did not work; others said they did not have the money to buy phone cards.

James Lynch, Amnesty's researcher on migrants' rights in the Gulf, said there were problems with phone lines in and out of the centre when the organisation visited the 1,600 detainees in March 2013.

"Many of the men and women we spoke to were also very unclear about why they were being held and what steps needed to be taken for them to leave the centre," Lynch said. "Not being allowed to have mobile phones clearly exacerbated this problem as it made it much more difficult for them to contact family, lawyers, embassies or friends in order to resolve their situation."

There are no official figures on Qatar's deportation centre, but up to 95% of the 400 women held there when Lynch visited were domestic workers.

"Men and women can sit detained in this jail for months, and some for over a year," a witness told the International Trade Union Confederation (ITUC) in its report, The Case Against Qatar, released in March. "There is so little room that women are sleeping in the hallway on mattresses, or mattresses are put under the beds to accommodate more human bodies. The vast majority of these men and women are not criminals. They are victims of a sponsorship system that is not only abusive but is modern day slavery."

More than 2,500 Indonesian maids a year have fled from abusive sponsors, according to the ITUC. Some women have fled abusive employers who have beaten or sexually assaulted them, only to be stranded in the centre because they do not have their passports or the correct paperwork.

According to Amnesty, the domestic workers it met in the deportation centre were being held there for breaching the terms of the sponsorship. Lynch said deportation orders were received for working for someone other than their appointed sponsor, overstaying their visa, or for leaving their sponsor without permission.

A study by the Journal of Arabian Studies in June 2013 found that 90% of low-income workers surveyed in Qatar did not hold their passports.

In January several recruitment agencies contacted by phone told a Guardian reporter posing as a would-be client that they routinely withheld the passports of migrant workers. "We keep them of course, this is the normal thing in this country," a representative of one agency said. "All companies keep all the employees passports."

Amnesty and the ITUC are pushing for Qatar to end the kafala sponsorship system and give domestic workers legal protection for basic human rights.