The body said that in countries such as Pakistan, Nigeria and Egypt -- where Islam is the dominant religion -- Christians in the minority can "often feel abandoned and isolated."
The Council's report warned that an "increasing trend among Islamic communities, sometimes promoted from outside, for implementation of Sharia (Islamic) laws, has created an environment of fear and insecurity among Christian minorities" which it says experience discrimination.
"Matters are further complicated by a view in some Muslim circles that Christians are... a legacy of the colonial past. They are often blamed for globalisation that is seen as a form of recolonisation by the Christian west," the report says.
But the Council found that Christians often respond "to the presence of holy warriors with equally militant crusades."
In such circumstances, the Council warned mosques and churches "are increasingly used as platforms for promotion of political agendas," meaning that "both become targets when tensions rise."
The Council stressed that the solution lay in communication between members of different religions, saying "interfaith dialogue needs to be further promoted and strengthened."
But dialogue, it insisted should be "not only among progressives and academics, but also at local community levels, and it should reach out wherever possible to the extremist elements of religious communities in tension."
The full list of countries identified by the WCC as problem areas for Christians included Pakistan, Indonesia, Nigeria, Sudan, Ghana, Sierra Leone, Egypt, Lebanon, Palestine and Bosnia-Hercegovina.
The Council brings together 342 Anglican, Protestant and Orthodox churches from 120 nations representing some 500 million believers.
