Permanent Secretary, Mrs Virginia Mabhiza told reporters that the intruder appeared to have gained access to her office through the ceiling.
She said she is yet to establish if there are any missing documents or other valuables.
Mrs Mabhiza said she discovered some shoe prints bearing evidence of dust and debris from the ceiling.
Meanwhile, the CID team is said to have attended the scene this afternoon.
This is not the first time that these offices have been broken into as last year, the office of the Vice President and Minister responsible for Justice, Emmerson Mnangagwa was also broken into using the same modus operandi.
Last year's break in was the fourth at Vice President Mnangagwa's offices.
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