The railways operator has used drones to create an aerial plan of all trees within 60 metres of its tracks, comprising “hotspots” which include mature trees.
The programme to keep leaves and branches off the lines has already involved the destruction of thousands of horse chestnuts, ash, poplar and sycamore trees.
Network Rail, however, said not all the 10 million trees identified would be felled or pruned.
But the RSPB last night warned that such activity should only take place at this time of year – the nesting season – if trains were at imminent risk.
The warning follows a row in Bournemouth after the British Transport Police was called following complaints Network Rail was felling hundreds of trees along the railway line, prompting concerns about nesting birds.
Meanwhile felling along the trans-Pennine route from Manchester to Leeds was described by one passenger as resembling a “logging operation”.
Network Rail has previously said the green corridor along its tracks acts as a haven for wildlife.
An RSPB spokesman said: “Tree pruning and felling should be avoided at this time of year to avoid harming birds.