Unkovic submitted his resignation to the Commonwealth Court, but the reasons had not be made public, The Patriot News of Harrisburg reported Saturday.
Governor's office spokesman Kevin Harley said the state would move "as quickly and as responsibly as we can" to replace Unkovic, who had developed a reputation as thorough and someone who was listening to community members.
Harrisburg filed for bankruptcy in October, which prompted the state to send in Unkovic, a municipal bond lawyer, to act as the city's financial custodian.
Given his background, his connection to creditors was considered a possible conflict of interest.
He was also accused of being too slow, asking the court for a month delay to submit his restructuring plan for the city.
"He is not out to campaign for office, let the town meetings to the candidates … . He is much behind schedule," said state Sen. Jeffrey Piccola, R-Dauphin County.
The plan Unkovic submitted was also deemed incomplete, as he said he could not determine what creditors would have to contribute until he knew what sums could be raised raise through the sale of various city assets.
But the man the newspaper called suspiciously connected to city creditors, had persuaded some critics.
"David Unkovic won over many residents who were cynical and wary of him. He won us over by being honest and listening to the community," said Alan Kennedy-Shaffer, founder of community group Harrisburg Hope.
One comment stood out, the Patriot-News said. In an interview, Unkovic said, "I'll say it point-blank, the creditors aren't giving enough. Creditors have to give more."
Last week, he became upset while testifying in federal court. He banged his fist on the witness stand and bemoaned city corruption and financial mismanagement.
After his comments, former Mayor Stephen Reed declined to comment on his track record on financial decisions.
"I have no doubt David Unkovic is a good man, but his comments were most regrettable," Reed said.