After Wednesday’s bond hearing and arraignment in federal court, Abbate’s attorney, Bruce Lyons, said that “depending on what’s asked of her, she will cooperate.”

Lyons said he did not understand why State Attorney Katherine Fernandez Rundle also filed theft charges against Abbate because they are virtually the same as the federal charges. “It’s unusual,” said Lyons, a longtime criminal defense attorney in South Florida. He said he hopes the state attorney’s charges will be eventually dropped as part of his effort to resolve the federal charges.

"The fact that the state attorney entered into the equation late in the game became an impediment to reaching a resolution of the federal case," Lyons said. "But I am hopeful that will happen."

In a prepared statement, Fernandez Rundle said: “There is no excuse for the theft of funds intended to heal the sick and the poor of our community. Every stolen dollar took a part of a sick person’s future.”

In a separate statement, U.S. Attorney Wifredo A. Ferrer said: “We will not relent in our efforts to charge individuals who use the health care system to line their own pockets. Our investigation remains ongoing.”

Abbate could see her federal sentence reduced depending on the extent of her cooperation with Assistant U.S. Attorney Michael Berger and agents from the FBI and the U.S. Department of Health and Human Services.

The center, which has three facilities, employs about 300 people and receives about $4 million annually from the federal government.

Abbate’s alleged misdeeds go back to 2008, when she earned $824,000 — several times what other Miami-area clinic heads earned. In a Miami Herald story about her sky-high salary in 2010, Abbate said her base salary was $275,000 and the rest was buying out “my pension and vacation time.” She told The Herald she needed additional money because “I had a sick child.”

In 2009, federal tax reports show, Abbate’s total compensation was $987,902, rising to $1.2 million in 2010. By contrast, the chief executive of Community Health of South Florida, with operations in South Miami-Dade and twice the revenues of Abbate’s center, earned $265,000 in 2008.

One of the allegations in the federal charges against her is that Abbate “obtained unauthorized compensation by causing MBCHC to issue unaccrued vacation pay to her that was not approved or authorized by the board of directors.”