The charity, which supports the persecuted church worldwide, estimates that hundreds of Eritrean Christian refugees have been subjected to terrible abuse after arriving in Egypt.
Egypt is the most popular destination for Christians escaping from Eritrea, one of the most hostile countries in the world for followers of the faith.
In Eritrea, Christians and evangelicals in particular are viewed as a threat to national security because of their allegiance to God before the state.
As a result, many of them are tortured and imprisoned for their faith in conditions described by Barnabas Fund as "horrendous".
Persecution has intensified in recent months after an Eritrean governor ordered a purge against Christians at the end of 2010.
The charity said hundreds of Eritrean Christians were risking their lives each month to enter Egypt, where they go in the hope of eventually being able to cross the border into Israel.
A Channel 4 documentary, "Breaking into Israel", last week charted the harsh 900-mile journey made by Eritrean refugees, some of whom die before reaching their destination. Some are shot dead crossing the Egypt-Israel border and others are caught and returned to Eritrea where they face torture and even death.
According to Barnabas Fund, the majority of the Eritrean refugees are Christians.
It warned that many of them were ending up in Egyptian prisons or being held hostage for $20,000 ransoms in the deserts of Sinai by Bedouin Muslim nomads who work with human traffickers.
According to the charity's estimates, there are currently between 500 and 600 Eritrean prisoners in Egyptian custody and as many as 200 in the hands of traffickers.
Hostages whose relatives are not able to stump up the ransom are being killed.
There are also unconfirmed reports that the hostage-takers are harvesting the organs of hostages who have been unable to secure the ransom for their release.
Abuse at the hands of the Egyptian authorities or Bedouin gangs includes rape and sexual harrassment, torture, beatings and slavery.
In Sudan, there are also reports of Eritreans being kidnapped from UN refugee camps.
The extent of the suffering is so bad that some Christians in the prisons have been driven to adopting Muslim names, as Muslims receive better treatment than Christians.
Through its partners, Barnabas Fund is helping to relieve the suffering of Eritrean Christians in prison by funding medicine and basic necessities such as food, clothes and sanitary products.
It has helped to secure the release of three refugees and paid legal fees to one prison to enable another 23 to be seen and registered by the UN Refugee Agency (UNHCR).
Its partners said the reason for the abuse was the refugees' Christian faith.
They said: "The situation on the ground is expected to keep on deteriorating while the number of refugees is increasing."
Barnabas Fund is appealing to Christians to pray for Eritrean Christians who have fled, as well as those who have stayed behind in Eritrea.
Dr Patrick Sookhdeo, International Director of Barnabas Fund, said: "The suffering of our brothers and sisters from Eritrea is unimaginable.
"They are in great danger from their government, which is one of the most severe persecutors of Christians in the world, and if they flee in the hope of a better life elsewhere, they face imprisonment, kidnap, torture, rape, beatings and even death.
"They desperately need our help today."