Cheryl Carter is standing trial along with Brooks at the Old Bailey, Britain's top criminal court, charged with conspiracy to pervert the course of justice.
Carter maintains that the notebooks, numbering around 30, were hers and that all Brooks' possessions were returned to the News International office.
She is alleged to have disposed of the evidence just hours before Rupert Murdoch was forced to close flagship tabloid the News of the World.
Carter told police that the notebooks dated form her time as beauty editor.
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"Anything that was left just went back."
A News International archivist on Monday told the court that he had been asked to retrieve his then-boss Brooks' notebooks, hours after former Sun editor Andy Coulson was arrested for hacking.
Nick Mays said Carter requested the boxes on July 8, 2011.
Coulson went on to became Prime Minister David Cameron's director of communications after leaving the Sun.
Brooks, 45, of Churchill, south England, and Carter, 49, of Chelmsford, south east England, deny the charge of conspiracy to pervert the course of justice.