Duff started last weekend's 2-2 draw at Peterborough following a short spell on the sidelines with a hamstring problem but suffered a calf injury early in the second half.
The 35-year-old was replaced by David Edgar and Clarets boss Sean Dyche is not hopeful over his prospects of facing Wanderers.
"Duffo is unlikely," he told his club's official website. "He has a calf strain and that will continue to get checked."
Fellow defender Ben Mee remains out with a knee problem but Dyche is otherwise boosted by a clean bill of health.
Top scorer Charlie Austin marked his return from a month out with a hamstring complaint by finding the net inside the first minute at London Road.
Fellow striker Sam Vokes returned unscathed following his goalscoring exploits with Wales in midweek.