The Stefanos Foundation also said discrimination against believers was a significant reason why Christians in many African countries were fleeing their homelands, because they are like "sheep to be taken to the slaughter".
On Thursday a multi-faith memorial service in Malta was held for 24 of the 800 migrants who died in the Sunday ship disaster.
They died when the boat they were travelling in sunk trying to cross the Mediterranean Sea to reach Europe. It's the worst recorded migrant ship disaster ever. So far, approximately 1800 migrants have died this year.
The charity's calling on the West to invest more into Africa to curb the need for people to leave, and is urging Christians to pray against the persecution of African believers and for increased long-term economic opportunities in the continent.
Mark Lipdo, Programme Coordinator at the Stefanos Foundation, told Premier's News Hour: "We are like sheep to be taken to the slaughter. We see people persecuted, from losing their loved ones to losing their property, and they have no dignity at all. Yet, their stories are not told in the West.
"And those are the ones that still seek... the West, and yet they are the ones who are denied entrance into the Western countries. Most of them have been sunk into the Mediterranean today.
"Africa is presently at war within itself. African young people have no love for their own continent. Young Africans see more hope in the Western countries than their own continent.
"If there's anything the West can do it is for them to help Africans take pride in its own its own continent. We see the West pumping a lot into China, for instance. African countries, particularly the Black world, have not been given such opportunities."
EU leaders including the UK Prime Minister David Cameron have been meeting in Brussels today, to discuss how to stop the migrant crisis. They've discussed launching full military action against human traffickers, and increasing the funding for search and rescue operations.
On Tuesday, Italian police arrested the ship's captain, who survived, and charged him with reckless multiple homicide and people trafficking. A crew member who survived was also charged with people trafficking.
Listen to Mark Lipdo speaking to Premier's Aaron James: