A spokesman said “a small quantity of drugs” was found in the 2 Marsham Street estate in central London on 3 May.
The incident came three days after Sajid Javid replaced Amber Rudd as Home Secretary after she resigned over the Windrush immigration scandal.
Security guards are believed to have discovered the stash of the highly addictive drug in a disabled loo.
The spokesman said building security referred the incident to the police who came to the Home Office and removed the drugs.
Scotland Yard decided to take no further action, he added, but could not explain why.
The revelation comes on the same day Mr Javid tweeted a picture of himself with a sniffer dog at Heathrow Airport, praising him for helping to sniff out “drugs, cash and illicit goods”.
The Home Office is in charge of leading the war on illegal drugs in the UK and employs 5,000 staff at its Marsham Street headquarters which is also shared with Defra and the Housing department.
However, the drugs were found in the Home Office section of the premises.
An insider told the Daily Mirror: “Everyone in the building is talking about this.
“We’re the lead department in the war against illegal drugs so it’s hugely embarrassing when they’re found under our noses.
“Our job is to break the bad guys, not to feature in an episode of Breaking Bad.”
Visitors to the building have to go through airport-style security, including body and bag scans.
However, staff with passes can walk straight through automatic gates without having bags searched.
The Home Office spokesman added: “We take incidents of this nature extremely seriously, always ensure that proper procedures are followed and take appropriate action based on the advice of the police.”
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Scotland Yard confirmed officers seized the drugs and took them to a local police station.
“Advice was provided to security staff. no suspects have been identified at this time,” a spokesman added.