The whale was caught in waters west of Iceland by whalers on board the ship Njordur, one of three vessels taking part, the marine scientist in charge of the controversial hunt said.
"They have caught the first whale," Gisli Vikingsson, of the Icelandic Marine Research Institute, told Reuters.
"It all went very well. Now they are doing measurements and research," said Vikingsson, on board one of the other two boats.
The three whale boats left port in the early hours on Sunday after receiving their hunting permits on Friday, for what the authorities have described as scientific purposes, primarily the impact on fish stocks.
Commercial hunting of whales has been outlawed since 1986 because seven of the 13 great whale species are endangered.
Iceland, which ceased whaling in 1989 under international pressure, says it must control whales to protect fish stocks and protect the livelihood of its fishermen.
An estimated 43,000 minke whales are believed to live in Icelandic waters, eating two million tons of fish and krill every year.
Whale meat not needed by the scientists aboard will be sold in Iceland's restaurants.
State Department spokesman Richard Boucher said the United States was "extremely disappointed" with Iceland's decision.
"I am sickened to hear this news"
Jill Sanders, International Fund for Animal Welfare
He said hunting the whales would "likely trigger a review by the Department of Commerce of Iceland's lethal scientific whaling process programme for possible certification under the Pelly Amendment".
The Pelly certification authorises the president to use his discretion to ban imports of products from a country cited as undermining an international conservation regime, such as the one maintained by the International Whaling Commission.
Environmentalists were also outraged at the catch. "I am sickened to hear this news," said Jill Sanders of the International Fund for Animal Welfare.
"We had really hoped Iceland would rethink this decision - until now," she said.
Sanders was among the opponents who had gone out to sea, trying to track the whale boats but was back in Reykjavik when the first catch was reported.
"They obviously waited until the cameras were gone. What are they trying to hide?" she said.
Environmental campaign group Greenpeace's vessel Rainbow Warrior has set course for Iceland from the South Atlantic, and is expected to arrive towards the end of August.
Greenpeace fears Iceland's resumed whale hunt, which will continue after the catch of the first minke whale, could be a first step towards the resumption of commercial whaling.