Bharara criticised Cuomo for dissolving the commission in exchange for new laws, which were approved aspart of a broader deal on the new state budget.
The top Manhattan federal attorney is now taking possession of all the case files that belonged to the commission that had been formed to Investigate Public Corruption in the state.
"If you begin investigations and you begin them with great fanfare, you don't, I think, unceremoniously take them off the table without causing questions to beasked," Bharara said in an interview to a radio show.
When asked if he would be opening a formal investigation into the governor's actions, Bharara said, "I'm not going to prejudge what we'll be looking at, what we'll be investigating and where the facts will lead."
The unusual public confrontation between two of the state's most powerful officials broke out two weeks after Cuomo decided to dissolve the anti-corruption panel.
The governor had appointed the panel last year to develop reforms to state law that would protect against corruption in Albany, the capital city of New York.
Bharara had this week written to 24 members of the commission and said that the panel's chairmen William J Fitzpatrick and former state and federal prosecutorin Manhattan Milton Williams had agreed to turn over the files.
Cuomo tried to play down the dissolution of the panel, also known as the Moreland Commission, as an expected and inconsequential step.
He said he neverintended to create what he called "a perpetual bureaucracy" to investigate wrongdoing.
The New York Times said the confrontation followed a request from Bharara's office to top commission officials asking them to refrain from destroyinginvestigative files.
Bharara's comments were unusual given that the US attorneys rarely speak out so forcefully about an elected official who is not adefendant in a pending case. In the interview, Bharara rebuked the decision to shut down the commission in exchange for the new laws, which were approved aspart of a broader deal on the new state budget.
"It was disbanded before its time," he said. "Nine months may be the proper and natural gestational period for a child, but in our experience it is not theamount of time necessary for a public corruption prosecution to mature."
Asked about Bharara's comments, Cuomo indicated he did not understand what the fuss was all about, saying that the commission was temporary in nature and itsmission was to prod reluctant lawmakers to pass new laws.
"I don't believe we needed yet another bureaucracy for enforcement," he said. "We needed laws changed, and that's what Moreland was about."
Asked if he had "bargained away" corruption investigations to strike a deal with lawmakers, as suggested by Bharara, Cuomo did not contest thatdescription.
He said: "That's what it was by definition. Nobody is going to be indicted tomorrow and nobody is going to be dragged away in handcuffs.
"But there are matters thatclearly need further scrutiny by a prosecutorial agency, and I think Preet is absolutely the right guy to do it."
Bharara has played a significant role in the prosecution of India-born former Goldman Sachs director Gupta on insider trading charges.
Bharara's office also filed a re-indictment in March against Khobragade on visa fraud charges.
Khobragade, former Deputy Consul General in New York, was arrested on December 12 on charges of making false declarations in a visa application for her maid, which had triggered a row between the two sides.