The Lambeth Conference, a once-a-decade gathering of the world's Anglican bishops, has left the Church of England with a £1.2 million deficit.
The shortfall will be discussed on Monday by the committee that manages the Church's finances.
More than 200 bishops refused to attend last month's conference, leaving organisers with a large bill.
A spokesman said that the Archbishops' Council, the Church's executive body, has agreed to meet part of the costs with an interest free loan.
"Organising something on the scale of the Lambeth Conference will inevitably result in a small deficit sometimes.
"The Archbishop's Council met last week to propose a solution," the spokesman said.
The boycott was over the Church's liberal approach to gay clergy and same-sex marriage.
American priest Gene Robinson's ordination as the first openly gay bishop in 2003 sparked the divide.
The leaders of the Anglican provinces of Nigeria, Rwanda, Kenya, Uganda and the Anglican diocese of Sydney, Australia all boycotted the conference.
Last month they launched a breakaway movement for traditionalists, the Global Anglican Future Conference.