Otherwise, Hoeness added that Blatter must be removed from office.
The world governing body endured a damaging 2011 as it became mired in a bribery scandal and beset by allegations of corruption.
In an interview with the Suddeutsche Zeitung, Hoeness said: "Blatter has to explain in the next twelve months clearly how it will dry out the swamp and, if he fails, we must find an opportunity to remove him."
The Bayern chief added: "There is something new every week."
FIFA have created an Independent Governance Committee (IGC) which is mandated to propose reforms to the game's world governing body in the wake of last year's scandals.
Former FIFA presidential candidate Mohamed Bin Hammam was handed a lifetime ban for bribery in July, while Jack Warner, a FIFA vice-president and president of the confederation governing football in North and Central America and the Caribbean (CONCACAF), resigned from all football activity in June having been charged with the same offence.
The IGC does not contain a representative from Transparency International however, after they expressed concerns earlier this month that committee chairman Professor Mark Pieth had been appointed by FIFA, and was being paid by them.