The 60-year-old looked straight ahead as Victorian Court of Appeal justices Stephen McLeish, Maree Kennedy and Stephen Kaye handed down their decision on Friday morning.
He was seeking to overturn drug trafficking and importation convictions on three separate cases - known as Orbital, Magnum and Quills.
The court ruled the appeal on the Quills brief was allowed, with the charges set aside and Mokbel acquitted.
But he will face a re-trial on the Orbital charges, while he lost his appeal on the Magnum brief.
Mokbel had claimed he suffered a substantial miscarriage of justice because of barrister-turned-informer Nicola Gobbo.
Ms Gobbo was registered as a Victoria Police informer from 2005 to 2009 and was acting as Mokbel's lawyer for four years before he fled to Greece in 2006.
She continued to advise him when he was extradited back to Melbourne in 2008.
Mokbel's barrister Tim Game SC argued the evidence against his client was "corrupted" because Ms Gobbo encouraged her clients to make statements against him.
Prosecutor David Glynn said Ms Gobbo was not acting as Mokbel's legal representative at the time he pleaded and, while the cases against him were weakened, they were still viable.
He also argued there should be a retrial if Mokbel's appeal was successful, but Mr Game said that should not happen because Mokbel had already served a large portion of his jail term.
Mokbel served 18 years behind bars before being released on bail in April.
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