The proposal would have involved professionals such as doctors, lawyers and teachers being given top-up training to entitle them to work in Britain.
The Church of England Synod, meeting in York, rejected a proposal to fund the scheme, suggesting it could be more far-reaching in future.
The Reverend Canon Simon Butler, who made the proposal, admits the Southwark Diocese is "disappointed" its initiative was blocked.
He told Premier: "We saw a particular need that could be addressed by the church.
"Those in the debate who didn't agree didn't do so because they thought it was an unworthy idea but they thought there were bigger and broader things we could do."
At the end of the debate, the Church of England restated its support for work to help refugees and endorsed a range of activities carried out by Anglican churches.
Simon Butler said: "While it has ended up in what could be seen as just a set of warm words, I think the church already does a lot more than that.
"They reflect an awful lot of action and a commitment to do more in the future."
But he concedes he would have preferred it if the training scheme had won the support of General Synod.
Simon Butler admitted wryly: "One of the people who spoke in the debate said 'we asked for an orange and you gave us a lemon'."
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