Police Scotland said they were called at around 8.50pm on Tuesday.
A Police Scotland spokesman said: “We were called to the Palace of Holyroodhouse, Abbey Strand, Edinburgh, around 8.50pm on Tuesday March 23, following a report of a suspicious item. Following examination by Explosive Ordnance Disposal (EOD), it was made safe.
“A 39-year-old man has been arrested in connection with the incident. There was no threat to the public and inquiries are ongoing into the full circumstances.