On Tuesday night, environmental protesters hooked themselves up to the ship's mooring lines to stop it leaving. They were later arrested by border guards and fined.
Greenpeace said the activists had moved in when they heard the ship, which they have tried to blockade by anchoring a protest vessel nearby, was about to sail.
Trafigura, the Dutch-based oil trading firm which had chartered the ship, issued a statement late on Wednesday denying that the vessel had been impounded and said it had commissioned an international inquiry to examine the Ivory Coast incident.
Thousands of people in Ivory Coast have suffered vomiting, stomach pains and other symptoms caused by toxic fumes from waste from the ship in late August. The incident has stretched the country's health services and forced its cabinet to resign.
Estonia's Environment Ministry said tests of the Baltic waters around the vessel had shown disturbing results.
"Preliminary analysis shows that it contains similar substances as those in the Ivory Coast," a spokesman said.
Trafigura, however, disputed the findings.
"The waste on the Probo Koala in Estonia is not the same waste as discharged in Adidjan," it said in the statement.
The firm has described the waste dumped in Ivory Coast as "chemical slops", a mixture of gasoline, spent caustic soda and water and said it was a normal by-product of cleaning tanks used to transport fuel.