The group said “at least three known swift nesting holes were filled with mortar”, which it claimed was done “despite local campaigners identifying at least nine nesting sites”.
Campaigners said they provided “38 pieces of evidence” of swift nesting sites.
Rob Pownall, from Protect the Wild, said: “Network Rail has said it is willing to work with local groups and improve the site for swifts.
“If that is true, then it should start by undoing the damage that has already been done. Future nest boxes do not replace destroyed nest sites, and they do not help birds returning right now.
“This should never have happened. But it can still be put right.”