The Natural Resources Department launched the controversial program in April 2010, offering trappers $20 for each coyote pelt.
The move came in response to fears that the animals were becoming more aggressive toward people.
The government says it paid out $66,800 for the 3,340 pelts it received in the most recent trapping season, which ran from Oct. 15, 2011 until March 31 of this year.
It says 403 licensed trappers took part in the program, up from 366 the season before.
In October 2009, a young Toronto woman was fatally mauled by coyotes while hiking in Cape Breton Highlands National Park.
Taylor Mitchell's death marked the first recorded fatal coyote attack in Nova Scotia, and only the second in North America.