Suffolk Downs, the East Boston racetrack competing to build a resort-casino, has been fined $1.25 million for discharging horse manure, urine and pollutants into tributaries of the Boston Harbor, according to court records filed in US District Court in Boston Wednesday.

The racetrack agreed to a consent decree that was filed with the court after federal officials began investigating high levels of bacteria and fecal matter in the wetlands around the racetrack in 2008.

According to a complaint filed with the court, the illegal discharge had been occurring since at least 2006 and possibly as early as 2004, and may have continued up until last year.

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The racetrack had no permit allowing it to discharge into the waters. It has since applied for one, but that request is still pending.

Chip Tuttle, the chief operating officer for Suffolk Downs, today issued a statement in which he said the company has already spent millions of dollars to improve its drainage system in recent years.

“Suffolk Downs has worked cooperatively with federal and state environmental agencies since this issue first surfaced five years ago and we have already taken substantial measures, including construction of a new $3.5 million drainage system in our barn area, to address the conditions and bring us into compliance,’’ Tuttle said in the statement.

He added, “We are confident that, in addition to our on-site improvements, our new walkway project in Belle Isle Marsh, and our water testing in the Mystic and Saugus rivers will contribute to a better environment in our area for the future.”

The consent decree, filed under the federal Clean Water Act, requires that the racetrack develop a proper stormwater and discharge management plan for the facility, as well as paying the fine with potential interest dating back to 2008.