Senior aid workers in Takoradi said they heard the captain radio that he was heading for Lagos. The vessel, a Nigerian freighter, Bulk Challenge, was seen leaving the port last night but it was not clear what direction it was headed.
Contrary to reports by port workers, government officials said that not all of the approximately 4,000 passengers had been briefly taken ashore. Security officials, fearing a stampede, had stopped the shore transfer and only the very ill were examined in tents erected on the quayside.
Nearly all the passengers, who are fleeing violence and anarchy in Monrovia, Liberia's capital, are unwanted by the country's neighbours who are tired with its six-year-old civil war and refugee problem.
However, some 200 passengers escaped from their eight-day ordeal on the Bulk Challenge when they jumped on to a barge in Takoradi and refused to reboard, officials said. They were still on the barge last night and were expected to be taken to a refugee camp near the capital Accra.
Ghana, saying it did not wish to encourage an exodus of refugees from Liberia where a six-year-old civil war has flared again, insisted the freighter leave after passengers received provisions and medical care.
"Care must be taken in order not to create a panic situation in Monrovia which will unduly generate more exodus of Liberians into neighbouring countries which are already saddled with playing host to hundreds of thousands of Liberian refugees," the Foreign Ministry said in a statement.
It cited the need to avoid undermining decisions taken last week on halting renewed civil war in Liberia by the Economic Community of West African States (Ecowas) of which Ghana holds the presidency.
At least three people have died on the boat - two said to have been shot by Nigerian peacekeeping troops on the freighter during an attempted mutiny. A woman died of internal bleeding.
Senior Nigerians said yesterday that its military government might offer a haven.
As Sierra Leone blocked another vessel with 700 refugees off Freetown, there were signs of international anger at the treatment of the Liberian refugees, particularly the freighter passengers, many of whom are sick, suffering diarrhoea and packed together on board with only one toilet.
The United Nations High Commissioner for Refugees, Sadaka Ogata, said: "Unless the door is open to them, a lot of people, many of them women and children, may die." She said the UNHCR was prepared to help countries that grant asylum to the Liberians.
Emma Bonino, the European Union's humanitarian affairs commissioner, said: "I am deeply shocked at the sight of thousands of helpless and hopeless civilians who are being sent from one port to another, and denied the right to proper refuge and assistance."