Kevin B. Carle, 44, was charged with a federal misdemeanor for violating the Endangered Species Act by "knowingly harassing, pursuing and harming whales," the Anchorage Daily News reported Thursday.
Prosecutors say Carle was piloting a 34-foot jet boat used to ferry loggers between logging camps and Craig, Alaska, in April 2008 when the first collision took place.
He rammed a second whale in September of that year, prosecutors allege.
Authorities would not say why they thought Carle rammed the whales.
"I would not even want to speculate on the motive," Julie Speegle, a spokeswoman for NOAA Fisheries in Alaska, said. "Suffice it to say that, according to a witness, it was intentional."
A plea agreement calls for Carle to plead guilty in exchange for two years probation and a $1,000 fine, the Daily News reported.