According to Key Travel, new surcharges announced last week by Virgin Atlantic and British Airways have increased the cost of flights from London to Cape Town by £104, from London to Entebbe by £50 and from London to Bangkok by £69.
"Our charity clients are looking at ways to deal with the problem by making cuts elsewhere," said Ajay Sodha, managing director of Key Travel.
A spokesman for Christian Aid said: "We'd rather be spending money on things other than fuel surcharges, but the increase could help us to cut down on our fuel emissions."
A spokeswoman for World Vision said that 97 per cent of its staff worked in their country of origin.
"As part of our environmental audit, we are in the process of installing video conferencing facilities to reduce the number of flights we take," she said.