A joint venture between Aberdeen-based FirstGroup and Italian-owned train operator Trenitalia is due to launch on December 8.
But the Competition and Markets Authority (CMA) said it is investigating whether the Department for Transport's (DfT) decision to award the West Coast Partnership (WCP) franchise to First Trenitalia could lead to competition concerns.
The CMA will consider whether the contract will lead to a merger which could substantially reduce competition.
The case was referred to the watchdog by the European Commission.
In addition to running West Coast Main Line trains, First Trenitalia has also been appointed as the "shadow operator" for HS2 and will be responsible for new high-speed services, depending on the outcome of an ongoing review.
FirstGroup currently operates three UK rail franchises: Great Western Railway, South Western Railway and TransPennine Express. It also runs open access operator Hull Trains.
Trenitalia runs trains on the c2c line between east London and Shoeburyness in Essex.
Virgin Trains, a partnership between Virgin Group and Stagecoach, has run services on the West Coast line since March 1997.
The companies are suing the DfT over its decision to disqualify their WCP bid due to a row over pensions.