Chicago’s City Hall watchdog on Wednesday threatened to publicly call out Mayor Rahm Emanuel’s administration whenever it refuses to cooperate with investigations, suggesting the mayor is reinforcing “deep-seated doubts” about a city with a long history of public corruption.

The comments from Inspector General Joe Ferguson, written in his latest quarterly report, is the latest chapter in his struggle with the Emanuel administration over whether the watchdog agency can enforce its own subpoenas on city officials.

Last month, the Illinois Supreme Court ruled that Ferguson must rely on Emanuel’s administration to enforce subpoenas during inspector general investigations – even if the mayor or his cabinet members are the targets of those probes.

In Wednesday’s letter, Ferguson accused the mayor of hampering his investigations by refusing to back changes to the law that could give him greater independence and authority.

“[T]he Mayor and his Corporation Counsel can cut off access to the evidence needed to definitively determine who, or what, is responsible for possible waste, fraud, and abuse in City government,” Ferguson wrote. “That is true whether the transgressor is at the ground level, in middle management, or ensconced in the corridors of real power in City Hall.”

Ferguson has been asking for changes in city law that would protect his office from the political budget-making process, and would let him take investigation subjects to court for ignoring subpoenas, instead of relying on City Hall. But Emanuel, for his part, gave no indication on Wednesday that he would support broader powers for the city watchdog, as Ferguson has requested.

“The IG has the same power and capability [as] the state IG and the federal IGs have,” Emanuel said. “Now, I don’t think that they’re not capable of doing their jobs, and I think he’s a good IG, so therefore I think he can do his job.”

In his letter, Ferguson complained that Emanuel’s administration has previously refused to enforce the inspector general’s subpoenas, and sometimes simply doesn’t respond to its requests. From now on, Ferguson said he plans to let the public know whenever the mayor’s office isn’t cooperating.

“It’s the mayor who calls the shots at the end of the day, when – when things reach, uh, places that he does not want them to reach,” Ferguson told WBEZ in an interview Wednesday.

Emanuel’s top lawyers have backed the inspector general during previous subpoena fights, Ferguson said. But he stressed the need for his office to be independent in cases like the one that ended up before the Illinois Supreme Court, after former Mayor Richard M. Daley’s administration refused to enforce a subpoena on one of Daley’s former top advisers.