Dr McCarthy told the New York Times newspaper that he found the new patch of ocean during a trip earlier in August on board a Russian icebreaker.
Dr James McCarthy, an oceanographer, says he found a mile-wide (1.6 km) stretch of open ocean on a recent trip to the region.
Some experts believe the ice cap could disappear altogether by the end of the 21st Century. They point to the rapid thinning of ice in the Arctic as further evidence of global warming.
But other scientists are less sure. They say movements in polar ice regularly create gaps in the ice cap - including at the North Pole itself.
Dr McCarthy told the New York Times newspaper that he found the new patch of ocean during a trip earlier in August on board a Russian icebreaker.
"It was totally unexpected," he said.
Another scientist on the cruise, palaeontologist Dr Malcolm C McKenna, said the ship was able to sail all the way to the North Pole through only a thin crust of ice, and arrived on the spot to discover no ice at all.
"I don't know if anybody in history ever got to 90 degrees north to be greeted by water, not ice," Dr McKenna was quoted as saying.
"Some folks who pooh-pooh global warming might wake up if shown that even the pole is beginning to melt at least sometimes."
Ivory gulls
The scientists say the ice cap in the whole area was so thin that the ship had to sail for another 10 kilometres (six miles) to find ice thick enough for the passengers to leave the boat and walk on the ice cap, as they had been promised.
The party also saw ivory gulls flying overhead, which ornithologists say is a first for the area.
Dr McCarthy, who is working on studies for the Intergovernmental Panel on Climate Change (IPCC), says he has previously found the North Pole covered in some 3 metres (9 feet) of ice during the summer.
Despite the lack of agreement over whether the North Pole stretch of water was as a result of melting or ice movement, scientists do agree that the ice cap in general is shrinking.
Analysis of data gathered by US Navy submarines have suggested that the ice draught in the Arctic (the difference between the surface of the ocean and the bottom of the ice pack) has thinned by more than 40% over the past 40 years.