Here's some information on the ballast water treatment method that James mentioned. The paper is called Design and Implementation of a Continuous Microwave Heating System for Ballast Water Treatment, and is getting some press coverage as a possible solution to the ballast water spread of invasive species.
Press reports are a little contradictory on the cost although the paper itself says 'implementation of this system by itself would be prohibitively expensive' so it looks like the 'low operating costs' are only when compared to conventional heating methods which are even more expensive.
'Boldor noted that the high heating rates, low operating costs, and effectiveness in hazy water distinguish it from conventional heating methods.' From Science Daily
'Given the amount of energy it takes to heat the water, the system’s operating costs are currently impractically high. But it may someday be useful in conjunction with other, cheaper methods, Dr. Boldor said, killing organisms that those technologies cannot.' From the NY Times
But even so, it's good to have options. I'm curious what 'prohibitively expensive' actually means since ship owners have been getting away with doing nothing for, well, ever. I presume any cost seems like a lot. Suck it up ship-owning dudes (or, more likely, pass the cost on).