Disney previously postponed the project due to concerns over its $250 million budget, only to revive it again when actor Johnny Depp and director Gore Verbinski agreed to concessions to reduce the cost by around $35 million.
However, The Hollywood Reporter understands that effects-heavy production has returned to the $250 million region. The publication's sources also claim that filming is running behind its 120-day shooting schedule.
Verbinski, who has already been forced to remove a train sequence from the movie, could be asked to make further cuts with script revision said to be under way.
The director ordered the construction of period trains from scratch for the film, a move which has been attributed to the high budget. Parts of the costly set also suffered weather damage and required repair work.
The Lone Ranger is scheduled to finish shooting in August ahead of its release in July 2013.