The man said he deleted the emails, but claimed his boss didn't believe him.
He then accused his employer of invasion of privacy. After the confrontation, the man left the office - and was then sacked via a text message.
The graphic designer said his performance was also often criticised at work and that his employer had previously threatened to sack him during the 14 months he worked at the business.
Amber Traffic Management told the commission the man's termination came about "as a result of your serious misconduct and continuous failure to perform to expected standards, along with wilful or deliberate behaviour ... inconsistent with the continuation of your contract of employment".
Fair Work Commissioner Nicholas Wilson found the man did not intentionally breach company policies by sending work files to his private email and that there was no evidence that "even if they were [sent to a third party] that their distribution would have caused significant or irreparable detriment" to the company.
"[The employee] puts forward that he was looking for a new job and needed samples of his work for his employment folio," Wilson said.
"Due to his inexperience as an employee he did not realise that he could not use his work from Amber Traffic Management in that way ... The mere fact of [the employee] having endeavoured to prepare a work folio for consideration by prospective future employers, in and of itself is not a reasonable ground for his immediate dismissal."
As reinstatement would be inappropriate, Wilson ordered Amber Traffic Management to pay A$10,000 ($11,076) in compensation.
