New environmental reports released Tuesday show the first segment of the line in the Central Valley will cost between $10 billion and $13.9 billion, far more than the 2009 estimate of $7.1 billion.
The first stage of the line would stretch about 140 miles from just north of Bakersfield to near Merced.
Critics have blasted the rail line as a "train to nowhere" because the first section would link relatively small towns away from the state's major population areas.
State lawmakers who have supported California's ambitious high-speed rail project questioned whether the state can afford it.
Supporters of the rail projet said the private sector will be a significant source of funding and that the money will start flowing once work begins.
The Associated Press contributed to this story