The creatures, which also include badgers, great crested newts, and water voles, were found between Uxbridge and Hillingdon stations by Metronet crews.
They were discovered while the workers were doing £7.5m work to stabilise embankments and cuttings on the track.
The maintenance firm and English Heritage hope to have finished rehoming all newts over the next few months.
Excellent cover
A trackside habitat survey found that stretches of rough grassland and open habitats along the District line, between Dagenham Heathway and Upminster in east London, provided excellent cover for reptiles.
The common lizard, slow worm, stag beetle and grass snake were among those identified.
Bats were also found among trees along the track and more than 570 species of insect were identified.
The discovery of an active badger sett on an embankment north of Amersham on the Metropolitan line in Buckinghamshire almost affected attempts to replace track on the line.
The sett is now being relocated with help from Natural England (formerly English Nature).
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