Each company which locates and constructs a railroad across any highway shall construct it so as to cross over or under the same and may, under the direction of the Commissioner of Transportation, raise or lower the same at such crossing or change the location thereof and shall make and maintain such bridges, abutments, tunnels, arches, excavations, embankments and approaches as the commissioner orders and the convenience and safety of the public travel upon such highway may require; but the commissioner may, upon notice to such company and to the selectmen of the town or mayor of the city in which such crossing is situated, direct such company to construct its railroad at such crossing upon a level with the highway; but no such direction shall be given in any case except for special reasons, which shall be recorded in the records of the commissioner.