HS2 Ltd is spending more than £100m building a "shed" for bats, the chairman of the government-owned company said.
Sir Jon Thompson told a rail industry conference the bat protection structure in Buckinghamshire was needed to appease Natural England, as bats are legally protected in the UK.
Government adviser Natural England was contacted for comment.
The 1km (0.6 mile) curved barrier will cover the tracks alongside Sheephouse Wood near Calvert to prevent bats being disturbed by high-speed trains.
Sir Jon said there was "no evidence that high-speed trains interfere with bats".
"We call it a shed. This shed, you're not going to believe this, cost more than £100m to protect the bats in this wood," he said.
Other more expensive options, including a bored tunnel and re-routing the railway, were considered.
After receiving 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 local council did not approve the work, Sir Jon said.
"In the end, I won the planning permission by going above Buckinghamshire Council's head," he explained.
Buckinghamshire Council’s Peter Martin, who is deputy cabinet member for HS2, previously expressed "extreme disappointment" about the structure.
In March 2023, the council said HS2 was cutting back trees in Sheephouse Wood in order to protect the "Bat Mitigation Structure" and railway line.
Earlier this year, Mr Martin said: "We believe HS2 Limited is unnecessarily damaging Sheephouse Wood, a Site of Special Scientific Interest and Ancient Woodland."
Sir Jon claimed the issue was an example of the UK's "genuine problem" with completing major infrastructure projects.
He told the Rail Industry Association's annual conference that HS2 Ltd has been required to obtain 8,276 consents from other public bodies in order to build phase one of the railway between London and Birmingham.
He said: "People say you've gone over the budget, but did people think about the bats [when setting the budget]?
"I'm being trite about it, but I'm trying to illustrate one example of the 8,276 of these [consents]."
Sir Jon, who has led the project since Mark Thurston left his role as chief executive in September 2023, warned in January that the estimated cost for phase one has soared to as much as £66.6bn compared to the £37.5bn forecast in 2013.