The conspiracy charges facing the three carry terms of life in prison.
The conspiracy charge carries a penalty of five years in prison and a $250,000 fine.
The judge told jurors that they could move on to consider the other counts and return to the conspiracy charge later.
However, they were acquitted of a conspiracy charge in the case.
Five others face only a conspiracy charge carrying a maximum 20-year term.
On May 22, 2009, prosecutors dropped the remaining conspiracy charge.
But whatever went to the contras would fit into such a conspiracy charge.
Defense lawyers often attack conspiracy charges as unfair for just that reason.
But last month conspiracy charges against the two marines were dropped for lack of evidence.
The conspiracy charges, the most serious, carry a maximum sentence of 10 years.