Hunters from Iceland's Marine Research Institute have killed the first of 38 minke whales they intend to take from local waters over the next six weeks.
The scientists want to see what whales are eating
Whalers aboard the Njordur - one of three government-commissioned Icelandic whaling vessels - killed the animal in waters west of Iceland at about 1700 GMT on Monday.
Reports say the vessel's crew complained their hunt was initially hampered by two pursuing boats, hired by media crews and animal welfare groups protesting against the killing of the mammals.
The United States has expressed "extreme disappointment" over the killing, which it has warned could trigger a trade embargo against the country.
"We're extremely disappointed with Iceland's decision to begin a lethal research whaling program, which anticipates taking 38
minke whales," state department spokesman Richard Boucher said.
"Although the program is technically legal under the Whaling Convention, we've said many times that lethal research on whales
is not necessary and the needed scientific data can be obtained by well-established, non-lethal means.
"The taking of whales by Iceland will likely trigger a review by the Department of Commerce of Iceland's lethal scientific whaling process program for possible certification under the Pelly Amendment," he added.
The amendment states the secretary of commerce must alert the president of the United States to any undermining of an international conservation plan - in this case, the International Whaling Commission.
The amendment grants the US president power to ban imports from countries that are reported.
Monday's harpooning of the minkie whale represents the first killing of the species in 14 years, according to the marine scientist in charge of the hunt.
Iceland says whales have become so abundant in its waters since a worldwide moratorium on commercial whaling that they are threatening stocks of fish, including cod.
Protestors say Iceland wants to re-start commercial whaling
But the International Fund for Animal Welfare (Ifaw) says there is no scientific basis for the operation, and that Iceland cannot use science to camouflage its desire to resume commercial whaling.
Iceland's tourism industry has also criticised the hunt, fearing it could damage the country's image, and threaten the increasingly popular whale-watching business.
However, polls show three-quarters of Iceland's 290,000 population supports the resumption of whaling.
The environmental organisation Greenpeace has sent its flagship Rainbow Warrior on a mission to Iceland.
The ship is due to arrive in two weeks.