Jim Smith said Monday the arrangement with Bowden as head coach and his successor, Jimbo Fisher, as offensive coordinator isn't working.
"We've got too many bosses out there," Smith said.
"Jimbo is in a very, very tough situation where people assume he has a whole lot more authority than he really has," Smith told The Associated Press. "He's getting blamed for a lot of things that's just not his fault."
The Seminoles (2-3, 0-2 Atlantic Coast Conference) are off to their worst start since Bowden's first year at Florida State in 1976.
Bowden said Sunday that he has no plans of quitting anytime soon. His 384 wins are three fewer than Penn State coach Joe Paterno, the career leader in victories among major college coaches. Bowden turns 80 in just over a month, and has a contract that gives him the option to return in 2010.
And while the school's trustees don't have immediate authority over coaches, they have significant influence since they are in effect the boss of university president T.K. Wetherell, who makes such hiring and firing decisions.
"Everything is kind of up in the air," Smith said Monday. "T.K. really has to make that call. I think he's at a point where he's going to deal with it."
Wetherell, who played at the school when Bowden was an assistant coach in the mid-1960s, is also leaving as president when a successor is named. It was Wetherell who brokered the arrangement to bring Fisher in as the designated successor to Bowden and to run the offense after the 2006 season. As part of the deal, Fisher has a $5 million buyout if he's not head coach by January 2011.
Smith said Fisher should take over following Florida State's last game this season.
Smith said that arrangement has resulted in division among the Florida State staff, an accusation Seminole coaches have vehemently denied.
"I know coaches are sniping at each other and that's just terrible," Smith said Monday. "There are too many mixed signals."
He also said fundraising has slowed significantly, and the school has an obligation to fans and alumni to be competitive.
"I take absolutely no pleasure in this," Smith said. "I love Bobby Bowden, but I tell you what, I love FSU more."