Ali Mohamed Ali, 51, acted as a negotiator for pirates who snatched Clipper Group's 7,300-dwt multi-purpose vessel CEC Future in 2008.
He has been held in a Washington DC jail for more than two and a half years after helping seal a $1.7m ransom for the ship.
US district judge Ellen Huvelle told the jurors, who began deliberations last Wednesday, to decide on two remaining charges of hostage-taking and conspiracy to commit hostage-taking, the Guardian reported.
At the time of his 2011 arrest, he was the education minister in Somaliland, a breakaway region of Somalia, but had spent most of his adult life in the United States.
Ali argued he was just a translator, not an advocate for the gunmen.
Former Clipper Group CEO Per Gullestrup testified that he built up a level of trust with Ali.
