Emma Head submitted three claims for journeys on the London Underground between October and November 2024, The Telegraph reported.
Ms Head, who is the project’s chief railway officer, is one of the highest-paid officials in the government, appearing on the Cabinet Office’s most recent list of “high earners”.
It comes as the project has been criticised by MPs due to its ballooning budget. Originally estimated at £37.5 billion in 2009, HS2's projected cost has surged to between £67 billion and £83 billion, with some estimates even higher.

Critics argue the escalating costs could be better spent on improving existing rail infrastructure or other public services like healthcare and education.
In October 2023, the previous Conservative government announced the cancellation of Phase 2 of the HS2 high-speed rail project, which was intended to extend the line from the West Midlands to Manchester. This was primarily due to escalating costs.
The PAC has consistently criticised HS2's management, labeling it a "casebook example of how not to run a major project."
In February 2024, the committee reported that the project now represents "very poor value for money" following the cancellation of its northern leg, with total costs for delivering only Phase 1 significantly outweighing its benefits.
Official data released by HS2 last week showed a number of senior officials submitted small expenses claims of less than £10.

The Telegraph reported Ms Head, who is responsible for technical oversight of HS2, claimed three times for “travel on TFL to attend external meetings”. This included two claims for £5.40 and one claim for £8.50.
Early last year, Huw Edwards, the project’s stations delivery director, claimed £4.36 for a dinner “while staying overnight in Birmingham on HS2 business.”
Greg Smith, a Tory MP for Buckinghamshire, told the newspaper that the company should be more careful about how its executives spend public money.
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“HS2 is a project that we can’t afford as a country, but this Government is ploughing on with regardless,” he said.
“Every day that goes by, the cost goes up by millions, if not billions.”