Guinea-Bissau complained on Monday that its former navy chief had been "kidnapped" from its territorial waters by US federal agents investigating a trans-Atlantic cocaine trafficking scheme.

The United States had said Jose Americo Bubo Na Tchuto, a US-designated international drug "kingpin", was arrested earlier this month in "international waters" near the west African island nation of Cape Verde.

But Guinea-Bissau communications minister Fernando Vaz told a media conference that "Rear-Admiral Bubo Na Tchuto was taken in our waters".

"We have asked the attorney general to demand that his US counterpart explain the abduction because we will take appropriate legal action for the kidnapping of a citizen of Guinea-Bissau in his country," he said.

The indictment against Na Tchuto -- better known as Bubo in his deeply impoverished country -- and two other defendants alleges they plotted to aid cocaine shipments from Latin America reach their markets in the US and Europe.

All three were detained after an undercover sting operation that began around August last year, culminating in dramatic arrests by US agents on a boat off west Africa on April 2, the federal prosecutor's office for Manhattan said.

The Bissau government's complaint came as details of the arrest emerged in an interview broadcast on local television Monday with a companion of Na Tchuto who was detained with him and then released.

"I confirm that we were captured and forcibly taken to Cape Verde by US police," said Vasco Antonio Na Sia.

Na Sia said he had accompanied Na Tchuto and several others onto a yacht anchored in Guinea-Bissau waters that was supposedly carrying a group of US businessmen who wanted to meet the ex-navy chief.

Na Tchuto and his companions were offered champagne by one of the Americans but it suddenly became apparent all was not as it seemed.

"He went into the hold where 50 heavily-armed men where hidden. Instead of champagne, armed policemen came out, shouting 'Police! Police!'," Na Sia said.

"We were pinned on the deck and handcuffed. They then blindfolded us and drew all the curtains. I felt the boat take off."

The yacht took them to the island of Sal in Cape Verde, where Na Sia was freed by the US officers, who told him he wasn't "on the list of the people we were looking for".

An armed forces source said Na Sia and an uncle who was arrested with him, were being held at a military headquarters in Bissau, without giving the reason for their detention.

Guinea-Bissau, a country of just 1.5 million people, has suffered chronic instability since independence from Portugal in 1974 due to conflict between the army and state.

Drug traffickers have turned the state, sandwiched between Senegal and Guinea where the African continent extends the farthest west toward South America, into a transit point for the cocaine trade.