He said many Anglican immigrants arriving in Britain from the West Indies in the Fifties were not welcomed into the Church. The comments came as Bishop Jones delivered a human rights talk as part of the 10th annual Peter Heery lecture in the crypt of Liverpool's Catholic Metropolitan Cathedral of Christ the King.
"I think the Church could be much more welcoming to black people," he said.
"The origins of the black-led churches in this country was because people coming to us, especially from the West Indies, did not find a welcome in the Church at the time. Although nobody admits to being racist, there are undercurrents in all our institutions that make black people and all people of ethnic minorities feel they don't belong.
"The Church is not institutionally racist but there are subtle forces at work in every institution that keep some people out.
"On behalf of the Church of England I want to extend a welcome to people of every race into the Church," Bishop Jones added.
The bishop hit the headlines last weekend when it was revealed that the father-of-three daughters was to be featured alongside strippers and table- top dancers in a BBC series to be shown in the run-up to Easter.
Bishop Jones, a close friend of the veteran entertainer Cliff Richard, defended his decision, claiming he was in line with the work of Christ.Reuse content