9News understands images of an illicit substance were also allegedly found on the pilot’s phone.
The discovery was made after the flight landed in Melbourne from Bali.
The first officer, crew and passengers were all searched as part of routine screening when they landed at Melbourne Airport about 6.30am on May 23.
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An Australian Federal Police spokesperson said there have been no criminal offences or charges, but the first officer is the subject of an internal Jetstar investigation.
The airline declined to comment on the exact circumstances, instead issuing a statement.
“We have zero-tolerance towards pilots operating under the influence of alcohol or other drugs and always undertake testing in accordance with aviation regulations”, a Jetstar spokesperson said.