The EFE said that the church all across Egypt was united in prayer for the country and was looking to Christians worldwide to pray with them.
They are asking Christians to pray for wisdom for the present government as well as the future leadership of Egypt, the safety of young people demonstrating in Cairo's Tahrir Square, which includes some Christians as well as Muslims, and for change to come about peacefully.
The WEA said in a statement: "Nobody knows what the changes in Egypt will be, but evangelicals in Egypt know that God is in control.
"Though they are a small minority, they are deeply committed to being good citizens and contributing positively to the future health and development of their nation.
"The Christians believe strongly that most Muslims and Christians are united in their common concern for the welfare of the nation."
The EFE is tapping into its national prayer networks and it reports that evangelical, Coptic and Roman Catholics are uniting in prayer in homes all over the country for the welfare of the nation.
The UN estimates that around 300 people have been killed in unrest around the country. Egypt's Health Minister Ahmed Samih Farid said five people had died in fighting between pro- and anti-government protesters in Cairo.
Anti-government protesters are demanding the immediate resignation of President Mubarak, who has been in power for the last 30 years.
Attempts by the Muslim Brotherhood, the largest opposition group in Egypt, to carve out a role for itself in the future leadership of the country have raised concerns for the already persecuted Christian minority.
Barnabas Fund, which supports the persecuted church worldwide, said Christians would be even more insecure under an Islamist regime and in the worst may even be forced to flee the country en masse.
It said: "Egyptian Christians are already second-class citizens in their own country.
"They suffer severe discrimination in many areas of life, such as in education and employment.
"And if the Muslim Brotherhood were to seize power, they could rapidly be subjected to a raft of even more humiliating regulations designed to exclude and degrade them further."