Groups including The Dog's Trust and Battersea Dogs' Home told producers that they would no longer be involved with the show's Find A Dog A Home appeal after Channel 4 began to charge viewers to call in.
Following Paul's move from ITV, the show introduced a 10p-per-call information service rather than a number to contact the charities directly - resulting in a huge drop in the number of callers.
A source told the Sunday Mirror, "The new system meant viewers had to fork out for two calls - one to the information line and then to the charity."
"The charities had no choice. They work on small budgets and rely on donations so they don't want to alienate people who could help by charging them twice to get in contact."
A spokesperson for the show has explained that the show will be reverting back to the previous system from Monday.