The charges relate to the possession and distribution of allegedly illegal tape recordings.
These led to corruption and fraud charges against Zuma being dropped by the National Prosecuting Authority (NPA) on Monday.
Speaking outside Durban Central Police Station on Thursday, Kohler-Barnard said she had laid charges against Hulley for allegedly being in possession of illegal stolen recordings of intercepted telephone conversations.
"We have also laid a charge against the National Intelligence Agency (NIA)'s deputy director general for operations, Arthur Fraser," she said.
A national newspaper had quoted three independent sources identifying Fraser as the one who had passed tapes on to Zuma's legal team.
"As such we will charge him with illegally distributing intercepted communication.
"Firstly we have laid a charge of theft, alternatively possession of stolen property, against Hulley, relating to his alleged illegal possession of tape recordings that are the property of the state."
Kohler-Barnard said neither Hulley nor his client was a state official and Hulley appeared to have obtained the tapes specifically for the purpose of assisting Zuma.
Hulley and Fraser were not immediately available for comment.
Sapa
Did the NPA make the right call on Jacob Zuma? Ebrahim Moolla takes on Rebekah Kendal…
Check out our voter's guide to see where the different political parties stand on crime.
For the latest election news, features, profiles and more, check out our Election Focus page.