Burger King was among 70 major food brands backing the body's campaign, which launched this week.
However, the fast-food giant is understood to have informed the FSA it wants to end its involvement because of concerns over the impact that salt reduction could have on the taste of its food.
An FSA spokeswoman confirmed that Burger King had pulled out, adding that the decision was 'disappointing'. However, she said it would not affect the efforts of other fast-food outlets and manufacturers.
'You only need to look at McDonald's to see that fast-food restaurants can successfully promote healthy choices,' she added.
Insiders have suggested that Burger King's decision has come from the group's head office in the US.