The Rev Dr Richard Frazer, convener of the Church and Society Council of the Church of Scotland, also said voting to leave would be a denial of Britain's global humanitarian and moral values.
He said: "The European project is far from perfect, but in as much as it has successfully replaced bombs with bureaucrats it has enabled European citizens to enjoy unprecedented peace, stability and opportunity since the Second World War.
"The issues we face are ones that we have in part made for ourselves and, remaining within the EU, we have the influence to be part of the solution rather than simply standing in the wings and laying the blame with the others.
"To walk away would be a denial of the very humanitarian and moral values for which we stand as an active participant in global civil society.
"It is simply wrong and a denial of our history to believe that the challenge of immigration and the refugee catastrophe is someone else's problem.
"In reality, our actions going back to the First World War and more recently our invasion of Iraq in 2003 have contributed, at least in part, to the migration crisis we are witnessing today."
His words come as other senior churchmen, including former President of the Conference of European Churches Very Revd Dr John Arnold and the Dean of Coventry Cathedral Very Revd John Witcombe, wrote an open letter to The Times newspaper urging Britain to vote to remain in Europe next week.
Their letter said: "To leave the EU would be a vote against a community from which we have much to gain and to which we have much to contribute.
"Brexit would be a vote against ourselves: a political, economic, cultural and spiritual self-inflicted wound."
Also today legal experts from the Christian advocacy charity ADF International have said that police are investigating churches across Europe because of EU hate speech laws.
ADF International says a Christian's freedom of speech is under threat because of EU laws.
The former Archbishop of Canterbury Lord Carey also came out in favour of leaving the EU recently.
He likened Britain leaving to the Israelites being called out of slavery from Egypt.
