It comes after Southeastern marked low on national passengers satisfaction surveys and major disruption at London Bridge station which is undergoing refurbishment.
Sir Hendy said the chief executive of Network Rail is a “nice bloke” but “no one is listening because they can’t fix London Bridge”.
TfL are set to take over central London services of Great Anglia trains next month, with aspirations to run more rail lines.
A spokesman for Southeastern told the Standard: “We are really proud of our frontline teams and the work they do every day, helping hundreds of thousands of passengers.
“It is disappointing that Peter Hendy’s comments do not reflect their dedication and hard work.”