Fuad Shobaki, former financier to Palestinian leader Yasser Arafat, was imprisoned in May after Israel accused him of involvement in the so-called Karine-A affair.
Mr Shobaki has been held under international guard at a jail in Jericho, the only West Bank city not under Israeli control.
Israel said his release would violate a deal under which Israel relented in its demand that the Palestinian Authority (PA) extradite Mr Shobaki to face trial in Israel.
Senior aides to Mr Arafat, who must approve the release, said it was unlikely the prisoner would be freed because of international repercussions.
Ship intercepted
Fuad Shobaki was jailed under a US-brokered deal which ended a 34-day Israeli siege of Mr Arafat's headquarters in Ramallah.
Israel said the former Palestinian brigadier-general masterminded an attempt to smuggle 50 metric tons of arms and explosives to the PA on board the ship Karine-A in January, 2001.
Israeli special forces intercepted the vessel in the Red Sea before it could reach its intended destination.
The affair undermined the PA's credibility with Washington and Mr Arafat later "accepted responsibility" for the incident.
Mr Shobaki was sent to prison in Jericho, where he has been guarded by British and American officials.
'No evidence'
The Palestinian court ruled on Tuesday that there was no evidence against Mr Shobaki, endorsing the findings of a commission of inquiry set up by Mr Arafat following the affair.
Israel has reacted angrily to the decision, saying it violated agreements.
"The revolving door policy is still in effect. They [the Palestinians] arrest in one door and let out in the other door," said Raanan Gissin, an advisor to Israeli Prime Minister Ariel Sharon.
He said Israel would have the right to "pursue" Mr Shobaki if he was freed.
Aides to Mr Arafat, however, said the prisoner was unlikely to be released.
"If we remove Shobaki from where he is right now, he may be abducted or killed by the Israelis," Palestinian chief negotiator Saeb Erekat said.