Network Rail said it “recognised and respect” the concerns raised.
“We know how strongly people, locally and nationally, feel about the swifts at Chapel Milton viaduct as we approach nesting season,” a spokesperson said.
“High Peak Borough Council confirmed to us that we would not need listed building consent to reopen holes in the viaduct on Friday afternoon. Soon after, our contractors were able to carefully drill and reopened the holes.
“We recognise how emotive this issue has been and there is learning for us here, which we will take forward as part of our longer‑term approach.”
Rob Pownall, from Protect the Wild, said campaigners “turned concern into real pressure”.
“Swifts are one of the UK’s most rapidly declining species. They return to the same nesting sites year after year, and when those sites are blocked they cannot breed. Getting these holes reopened before the season was always the priority,” he said.
“There is still work to be done to ensure swifts are properly protected during future infrastructure works.”