The number of Eritreans persecuted for practising religions not recognised by the state is on the rise, Amnesty International (AI) says.
Gospel singer Helen Berhane was arrested last year
Over the past three years, more than 1,700 evangelical church members, including women and children have been arrested, their report says.
But Eritrean Information Minister Ali Abdu described the AI report as "unsubstantiated fabrication".
More than 90% of Eritreans belong to one of four recognised religions.
These authorised faiths are the Orthodox, Catholic and Lutheran churches and Islam.
The report says that for the last decade Jehovah's Witnesses have suffered severe persecution, but this has spread to other unofficial religions.
The report details the case of 30-year-old Helen Berhane, a well-known singer from the Rema Church.
She had just released a cassette of gospel music when she was arrested in the capital, Asmara, on 13 May 2004.
But as she refuses to abandon her faith and singing - despite promises of release if she does so - she continues to be held at Mai Serwa military camp in a metal shipping container.
Many prisoners are held in such containers, which are swelteringly hot during the day and freezing cold at night, with no washing or toilet facilities, the report says.
"The situation is critical and we are extremely concerned for the safety and wellbeing of hundreds of people facing this reality in Eritrea", said Kolawole Olaniyan, of AI's Africa programme, calling on the government all to release all those detained for their religious beliefs.
Other cases include individual arrests for possession of Bibles, prayer meetings at private homes, watching church videos, or for belonging quite simply to unauthorised religious minorities.
But the BBC's Ed Harris in Asmara says that Mr Abdu dismissed the report's criticisms.
"Who are these Amnesty International people? Who gave them the right to hand out qualification certificates?" the minister asked.
The report says that the lack of religious freedoms comes in a context of systematic violations of human rights and continued tensions with neighbouring Ethiopia.