A top Chicago Public Schools official is resigning amid another reorganization of the system’s leadership.

Chief Portfolio Officer Oliver Sicat submitted his resignation yesterday, but will stay with the district through March, said CPS spokeswoman Becky Carroll. The former principal and teacher will pursue other career opportunities, Carroll said.

Sicat was tapped by former schools chief Jean-Claude Brizard to run the Office of Portfolio, which oversaw the creation of new charter and magnet schools and managed the enrollment process. That office will now be absorbed into the new Office of Innovation and Incubation, run by Jack Elsey.

The departure and overall reorganization comes at a time when confidence in CPS is strikingly low.

After his election Mayor Rahm Emanuel cleaned house at CPS, claiming he needed to “hit the reset button on education.” Alicia Winkler and General Counsel Pat Rocks were the only two holdovers from the Daley era. Rocks retired last summer.

But today, just three of the eight people initially appointed by Emanuel remain. One of those three is Winkler. The other two are Carroll  and Chief Administrative Officer Tim Cawley.

A shake-up in school leadership is not uncommon when a new Chief Executive Officer is appointed. In 1995, when then-Mayor Richard M. Daley took control of the city’s public schools, his first CEO Paul Vallas restructured the system. Arne Duncan did the same in 2001, when Daley appointed him to succeed Vallas.

But rapid change in school leadership over the past three years has meant much more frequent, and costly, reorganizations. Principals, teachers and other stakeholders have grown more confused and frustrated as faces change and offices are renamed.

The departures come with hefty price tags for the cash-strapped school system.

Emanuel’s initial top two picks, Brizard and Chief Education Officer Noemi Donoso both left with substantial severance packages. Donoso left in late April, just shy of a year in office, and got half a year’s salary, or $134,000, and did not have to repay the $21,000 in relocation expenses, although her contract said she would. She also stayed on payroll for a month after her resignation.

Brizard’s high-profile exit is costing the district more than $300,000. He remained an employee through the end of December 2012 and gets a year’s salary, or $250,000, beyond that.

Carroll said current CPS CEO Barbara Byrd-Bennett, who took over for Brizard after he left in the wake of the first teachers strike since 1987, is still organizing her team.

Last month, the Board of Education approved the appointment of five new cabinet members. Two were promotions from within CPS.

Annette Gurley will take over many of the duties of the Chief Education Office, long considered the second in command at CPS. Her title will now be Chief of Teaching and Learning and she’ll oversee curriculum and instruction and other education-related services.

John Barker will be the Chief Accountability Officer overseeing testing, assessment and data. That position was previously empty.

Denise Little will be Chief of Networks, overseeing middle-management which deals directly with regional groups of schools.

Jack Elsey will run the Office of Innovation and Incubation, formerly Sicat’s Office of Portfolio. The office oversees the creation of new schools, the school enrollment process and other specialty and military programs.

The Office of Talent will continue to be run by Alicia Winckler; the Chief Administrative Office will continue to operate under Tim Cawley; Phil Hampton will remain in his post as Chief of Family and Community Engagement and Carroll will continue to run Communications.

An updated organizational chart outlining what other departments fall under these is not yet available, Carroll said.