HS2 boss Sir Jon Thompson revealed the structure is being constructed along a section of the £66billion London-Birmingham high-speed line.
He said it is needed to appease government adviser Natural England, despite there being "no evidence that high-speed trains interfere with bats".
Critics said spending by the government-owned company HS2 Ltd is "way out of control" and comes at a time when pensioners, workers, businesses and farmers have just been clobbered by a £70billion tax and borrowing Budget bombshell.
The 0.6mile-long mesh structure will be built where the high-speed line emerges from a tunnel in Buckinghamshire, to protect a colony of Bechstein's bats.
Describing it as a "blot on the landscape", Sir Jon said: "This shed, you're not going to believe this, cost more than £100million to protect the bats in this wood."
The curved structure will run alongside Sheephouse Wood, creating a barrier allowing bats to cross above the high-speed railway without being affected by passing trains.
Other more expensive options, including a bored tunnel and re-routing the railway away from the wood, were considered.
After the go ahead from Natural England for the design, HS2 Ltd was forced to spend "hundreds of thousands of pounds" on lawyers and environmental specialists because the council did not approve the work, Sir Jon said.
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