The stock was down about 13 per cent to $6.56 at mid-day on the Toronto Stock Exchange.
CEO Gary Kubera says the company is disappointed with the revised estimate, but noted Canexus has "established a state-of-the-art facility."
The first phase of the expansion is in the process of starting up and the company expects to load 14 unit trains, or about 30,000 barrels per day of crude, during February.
The project is expected to be complete later this year.
Canexus expects to fund the incremental cost from its committed credit facilities.