Authorities say the shark attack happened between Maui and Molokini. The shark bit his dangling foot while he fished with artificial lures to attract baitfish, a news release from the state Department of Land and Natural Resources said.
The man was identified as 57-year-old Patrick Briney of Stevenson, Wash.
His fishing partner in another kayak heard his screams.
"He paddled over and found him in that condition lying down. He applied a tourniquet on the leg that was wounded, and I guess somehow tethered his boat to his," said William Dunaway, a witness.
A nearby charter tour boat took them to shore, and the man was then taken to a hospital, the state said.
"He was missing his foot and his calf; most of it was torn off to the bone," Dunaway said. "We were all shocked. It was gruesome."
The kind of shark involved was not immediately available.
There have been 13 shark attacks in Hawaii this year, and this is the second fatal attack. In August, a German tourist died a week after losing her arm in a shark attack. Jana Lutteropp, 20, was snorkeling up to 100 yards off a beach in southwest Maui when the shark bit off her right arm.
Before Lutteropp's death, the last shark attack fatality in Hawaii was in 2004, when a tiger shark bit Willis McInnis' leg while he was surfing in Maui.
"We are not sure why these bites are occurring more frequently than normal, especially around Maui," said department Chairman William Aila Jr. "That's why we are conducting a two-year study of shark behavior around Maui that may give us better insights."
Officials say the study will focus on tiger sharks because they move around frequently and have been known to travel all around the waters of Hawaii.
The Associated Press contributed to this report.