Cooney, 27, has battled through degenerative problems in his knee over recent seasons and was on Wednesday taken to hospital to be treated for yet another setback.
Dogs officials revealed the bitter news for Cooney on the club's official website.
"Midfielder Adam Cooney is currently receiving treatment for an infection to his right knee," the Dogs said.
"Cooney was admitted to hospital yesterday to treat the infection and to receive intravenous administered antibiotics.
"This treatment will continue for the remainder of the week."
Cooney remains in hospital, declaring via his official Twitter account that the infection was from a cut.
The 2008 Brownlow medallist, who played 14 games last season, is expected to return to training next week.
But, with the Bulldogs' first home-and-away match, against Brisbane at Etihad Stadium, a little over a week away, Cooney seems an unlikely prospect.
Bulldogs football manager James Fantasia described the infection as a "minor setback" for the star ball-winner.
Cooney underwent a ground-breaking procedure late last year in Germany in an attempt to cure chronic swelling and cartilage problems in the knee joint.
The champion on-baller was then able to participate in the Dogs pre-season training over the summer for the first time in four years.