Christie told The Record newspaper's editorial board Thursday that the employee deviated from a storm plan at the last minute without the knowledge of New Jersey Transit executive director Jim Weinstein.
The governor says the unnamed employee was a civil servant and because of civil service rules, could only be demoted, not fired.
However, the New Jersey Civil Service Commission website makes no reference to NJ Transit and the agency's job applications don't mention civil service requirements.
Sandy's surge overwhelmed low-lying rail yards in Hoboken and Kearny, damaging 273 rail cars and 82 locomotives.
Information from: The Record (Woodland Park, N.J.), http://www.northjersey.com