Obama chose to order the State Department and Commerce Department to keep Iceland's whaling activities under review and to urge the government in Reykjavik to halt the practice.
"Iceland's actions threaten the conservation status of an endangered species and undermine multilateral efforts to ensure greater worldwide protection for whales," said Obama in a message to Congress.
"Iceland's increased commercial whaling and recent trade in whale products diminish the effectiveness of the (International Whaling Commission) conservation program."
After a pressure campaign by environmentalists, Commerce Secretary Gary Locke earlier this year certified Iceland under a domestic law that allows retaliation against nations that flout the IWC moratorium.
But Obama said in the message that "I am not directing the Secretary of the Treasury to impose trade measures on Icelandic products for the whaling activities that led to the certification by the Secretary of Commerce."
Instead, Obama directed US government officials to consider the appropriateness of traveling to Iceland, to raise the whaling issue with officials when they are there and to keep the situation under review.
Under a law known as the Pelly Amendment, countries that violate global fisheries conservation agreements are subject to economic sanctions but Obama's action on Thursday waived its requirements.
The International Whaling Commission imposed a global moratorium on whaling in 1986 amid alarm at the declining stock of the marine mammals. Norway and Iceland are the only nations to defy the moratorium openly.
Japan hunts more than 1,000 whales a year, a point of intense dispute with Australia. But Japan considers itself within the rules of the IWC by invoking a clause that allows a catch for scientific research.
Japan has actively campaigned to end the moratorium, saying that whaling is its cultural right. Environmentalists counter that whale populations are at risk and highlight the mammals' intelligence, saying the slaughter is cruel.
Iceland, which resumed commercial whaling in 2006, is seen as less entrenched in its position than Japan and Norway. Iceland, a country of 320,000 people, has a small market at home and its exports to Japan are uncertain.
Iceland's whaling company, Hvalur, suspended fin whaling after Japan's March 11 earthquake hit demand. Iceland killed about 150 fin whales and between 60 and 80 minke whales last year.
The United States has previously invoked the Pelly Amendment against Norway and Japan but it has not followed through on sanctions, hoping instead to use the certification as a means of pressure.