The case involves a suit by three black House members who are objecting to the districts drawn this year by the Republican-led Florida legislature.
Harris's spokesman, David Host, said although Harris feels duty bound to defend the state in the lawsuit, Democratic Attorney General Bob Butterworth is helping the three plaintiffs.
"For some inexplicable reason, Judge Andrews has asked Secretary Harris to explain why politically motivated forces included her in this lawsuit in the first place," Host said. "Now that she is involved in her official capacity as Florida's Secretary of State, Secretary Harris is duty bound by her oath of office to support and defend the existing laws of the state of Florida."
Harris and Butterworth are named as defendants in the lawsuit filed by Reps. Alcee Hastings, Carrie Meek and Corrinne Brown, D-Fla., who contend the new districts are unconstitutional.
Broward County Circuit Judge Lance Andrews said in his order that Harris' public role in the suit could create a conflict of interest in view of her campaign for a congressional seat in the Sarasota area. The three members of Congress are from other areas of the state.
Andrews also asked her to explain what authority she has to defend Florida in redistricting lawsuits.
A hearing before a three-judge federal panel continued Tuesday.
Democrats are hoping to persuade the judges that the redistricting map violates the federal Voting Rights Act by decreasing the chances of minorities to rise to political power.
American University history professor Allan Lichtman said the plan violates the rights of minorities no matter how you look at it and that computer studies back him up.
"By every measure, there is a (reduction) of black voter strength," he said. "No matter which test you're using, the changes are politically consequential."
He also said the plan would give Republicans 28 of 29 seats in a state that breaks just about even along party lines, as evidenced by the presidential election that President Bush won by 567 votes.
GOP Attorney Miguel DeGrandy questioned the reliability of computer studies that use past election results to predict future results.
2014: The Year in Music [PHOTOS]