A mistrial was declared for four former leaders of the Holy Land Foundation while a fifth had most charges dropped.
It was not clear if the prosecution would seek any retrials.
The jury forewoman admitted surprise at the action of the three jurors.
"When we voted, there was no issue in the vote. No-one spoke up any different. I really don't understand where it is coming from."
After a further one hour deliberation, 11 jurors said they would be unable to come to a unanimous verdict.
The charity leaders were accused of funding Hamas, which was designated by the US as a terrorist group in 1995.
The charity said it ran a legitimate operation helping Muslim families.
The prosecution argued Hamas controlled the charities to which $12.4m was sent between 1995 and 2001, when the Holy Land Foundation closed.
Khalil Meek, president of the Muslim Legal Fund of America, said of the result: "It's a victory for the Muslim community."