According to Christian Solidarity Worldwide, a religious freedom charity, the mother was detained in May and died earlier this week in Metkel Abiet, a desert camp in the Northern Red Sea Region.
Although the cause of her death is still unknown, the camp where she was kept is in an area known for its heat and dryness.
CSW has urged the international community to ensure that the government and its officials are made to account for the crimes perpetrated against Eritrean citizens.
Chief Executive of CSW, Mervyn Thomas, said: "CSW is saddened to hear of the death of Fikadu Debesay.
"Our thoughts and prayers are with her family at this painful time. We think particularly of her children, who are mourning their mother in the absence of their detained father, and of the other children whose parent or parents are unjustly incarcerated.
"It is alarming to note that conditions and treatment in detention are so inhumane that they can cause a mental breakdown."
A campaign of house to house raids targeting members of non-sanctioned churches was initiated in several towns this year. CSW said 23 Christians were rounded up in the capital city, Asmara during the first week of August.
It marks a significant crackdown that has been ongoing since May 2002 when the Eritrean government outlawed religious practices not affiliated with the Catholic, Evangelical Lutheran and Orthodox Christian denominations or Sunni Islam.
The number of Christians known to have been detained in desert camps and military facilities since May has now risen to 210.
Most were detained following raids on their homes, while a few were arrested at prayer meetings.
Like Debesay, several are parents, and according to local sources, over 50 children are currently without one or both parents as a result of these raids.