Elliott pleaded guilty to two charges, the others were dropped.
Waikato Police served papers on Elliott, who now lives in Papamoa, on March 29 to recover $60,000 they allege he spent on the school's credit card.
Hamilton Asset Recovery Unit officer in charge Detective Sergeant Craig Hamilton said the claim was lodged in the High Court at Hamilton by the Commissioner of Police under the Criminal Proceeds (Recovery) Act 2009.
Mr Hamilton said the civil claim was the result of further investigation by the Asset Recovery Unit (ARU) whereby restraint and forfeiture was sought on Elliott's assets so the Crown could recover the "misappropriated funds".
ARU national manager Detective Superintendent Peter Devoy said the criminal case was over, but the act ensured people involved in crime did not profit from those activities and allowed for civil action to be taken through restraining property and assets.
"In this case we intend to restrain property belonging to the offender and return the money to the Crown," Mr Devoy said.
The onus was now on Elliott to prove to the court he had not benefited from criminal acts, Mr Devoy said.
Mr Hamilton said the claim was in its infancy and he was not aware if Elliott had filed an opposition to it.
Elliott referred inquiries to his lawyer Mark Hammond, who did not return calls.
Elliott spent a decade at Hamilton's largest secondary school, Fraser High, where he introduced Saturday classes for failing students, banned cellphones in class to stop text bullying, allowed parents to do chores around the school to pay their children's fees and started a creche for teenage mothers.
Elliott, a former mayoral candidate and Justice of the Peace, was in charge of $10 million of public money.
At his sentencing in February, defence lawyer Michael Reed, QC, said Elliott had suffered a spectacular fall from grace.
"This man has suffered above and beyond. His career is shattered. He is no longer a school principal.
"Financially he is in a very precarious position. He had to move out of the area because of the attention."