The attack by hundreds of guerrillas of the FARC movement (Revolutionary Armed Forces of Colombia) on the Jurado base is being described as the worst defeat suffered by the country's navy.
The Colombian military say a counter-attack involving a battleship and hundreds of troops has successfully re-taken the base.
Jurado is only 30km (20 miles) from the border with Panama and the incident took place on the eve of a ceremony to mark the United States' handover of the canal to Panamanian sovereignty.
Maurice Perdomo, one of the marines who survived the attack, said: "We were attacked by 600 or 700 guerrillas with gas cylinders and bursts of M-60 (light machine-gun) fire."
Some reports say as many 65 of the government forces died in the raid on the base, used to patrol arms and drugs smuggling routes off the Colombian coast.
The Colombian navy said the raid was the work of "terrorists" .
The attack on Jurado, was one of several carried out by the FARC guerrillas in northwest Colombia in recent days.
US pull out
There are major security concerns in the area as US forces are due to pull out of Panama at the end of the year.
The Americans are said to be increasingly concerned that the withdrawal of US forces will leave Panama vulnerable to attacks.
The US army has warned that the Panamanian Defence Forces would be powerless to stop rebel incursions into Panama once American forces pulled out of the Canal zone.
"This is a conflict that is spilling across borders and there's nothing Panama can do to stop it," said Cynthia Watson, assistant dean at the US army's Washington-based National War College.
The FARC is holding peace talks with the Colombian government but has not declared a ceasefire.
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