The World Evangelical Alliance says Christians are "now at even greater risk" in Afghanistan after the takeover by the Taliban.
The WEA has expressed "deep concern" for the persecution of religious minorities, the suppression of women, and an increase in the drug trade and human trafficking.
It is calling on churches and Christians to pray for Afghanistan, those attempting to flee, and "especially for Afghan Christians and others who are vulnerable".
"We are very concerned about the recent developments in Afghanistan and the dire prospects for all those who do not fit within the Taliban's view of a society," said Dr Thomas Schirrmacher, Secretary General of the WEA.
"Women, who will be among those who have most to lose, will likely again be prevented from enjoying basic rights, including tertiary education, professional careers, and even freedom to move around on their own.
"What is less reported is the plight of religious minorities, including Christians, who have suffered severe oppression during the past twenty years and who are now at even greater risk."
He said that while it would be wrong to pretend everything was well in Afghanistan prior to the takeover, the situation for minorities is set to worsen.
"Converts from Islam have been killed in areas under the former official government, and war lords who controlled part of the country, and are now losing their power, were not much better," he said.
"The Constitution of 2004 stated that Afghanistan is an Islamic Republic with Islam as its state religion, leaving no place for religious freedom in the country.
"In reality, all religious minorities suffer in Afghanistan and will suffer even more now – including Muslim minorities like the Shiites and those Muslims who have became followers of Jesus Christ."
Schirrmacher said it would be too simplistic to regard the Taliban as only a small group of insurgents seeking to impose its will on society, and that public support for it has been "much more significant than Western countries thought, with many people even voting for them in elections."
He said he expected to see an increase in illicit trade and slavery.
"Taliban finance themselves to a large extent through all kinds of criminal means, especially drug trade and human trafficking. Selling girls into sex slavery is no problem for them, especially if they do not belong to their faith community," Schirrmacher said.
He added, "our hearts cannot help but ache for the many Afghans who are longing for freedom but once again have to live in fear within their own nation, as well as the many who have fled to other countries as refugees leaving behind everything."
"Join us in prayer for our brothers and sisters in Christ that they would be protected and comforted. Scripture reminds us that we are one body in Christ and 'if one part suffers, every part suffers with it' (1 Corinthians 12:26a). And let us pray for new hope for the whole nation that is facing a very dark moment at this time," he said.