What followed has included reports of grand jury subpoenas, a parade of members of the commission and its staff to Mr. Bharara’s office to be interviewed about the panel’s work and its shutdown, suggestions that the governor’s office has not moved fast enough in having subpoenaed documents turned over by the commission and the hiring of criminal defense lawyers by witnesses and potential targets, the governor’s office itself included.

But Mr. Bharara’s investigation into the disbanding of the panel, known as the Moreland Commission, took on a new and more volatile dimension on Wednesday, when his office warned that attempts by Mr. Cuomo or his allies to line up public statements supporting the governor from members of the defunct commission — the sort of coordinated political response for which Mr. Cuomo, a Democrat, is well known — could constitute criminal witness tampering or obstruction of justice.

The very public collision between Mr. Cuomo and Mr. Bharara, which comes a little over three months before the governor seeks re-election, is unlike any that Mr. Cuomo has faced in his political career.

As state attorney general, he led an investigation into then-Gov. Eliot Spitzer, damaging Mr. Spitzer’s reputation in advance of his later undoing in a prostitution scandal. Mr. Cuomo’s disdain for his fellow Democrats Eric T. Schneiderman, the attorney general, and Thomas P. DiNapoli, the comptroller, has been widely documented, but neither has publicly taken him on. This year, he outmaneuvered another Democrat, Mayor Bill de Blasio, over taxes and charter schools, but inflicted only glancing blows, and Mr. de Blasio this week felt compelled to defend Mr. Cuomo as “a person of high integrity” and “an agent of reform.”

No countermove in Mr. Cuomo’s extensive political playbook seemed to apply to his latest rival, Mr. Bharara: a federal prosecutor free of the co-dependencies that often lead Albany lawmakers to shy away from conflict with the state’s most powerful politician.