The Championship outfit recently confirmed losses of £36.5m, which in turn has resulted in speculation that they could be forced to sell their Scottish international striker.
However, following a meeting with the club's owners, Bowyer has been reassured that there is no financial need for him to part with the 23-year-old.
"January is coming so we need to know where we stand, both ins and outs, and that has been positive with regards to Jordan Rhodes," he told the Lancashire Evening Telegraph.
"It's still the case that he's not for sale and I'll start saying that again until the end of the January transfer window."
Rhodes joined Rovers from Huddersfield Town in August 2012.