Estonia's environment ministry said tests of the Baltic waters around the Probo Koala vessel, now docked in the country's Paldiski port, showed "disturbing" results and criminal police were sent to prevent it from sailing out to sea.
The move follows a request from Daniel Aka Ahizi, Ivory Coast's environmental minister and judge Fatoumata Diakite, who are in charge of an inquiry into the disaster, to immobilise the ship.
Piret Seeman, a spokesperson for Estonia's prosecutor's office, said the inquiry would find out "whether the ship had asked to leave the cleaning residue in Estonia, knew what the waste contained and wished to hand over residue that contains poisons".
At least eight people died and thousands fell ill after the ship, leased by Trafigura Beheer, the Netherlands-based shipping company, offloaded more than 500 tonnes of waste from the vessel in Ivory Coast.
A local company charged with disposing of the waste then dumped it on open-air rubbish tips in the commercial capital of Abidjan, a city of four million people.
The incident sparked widespread anger, stretched the country's health services and forced its cabinet to resign.
French embassy officials said on Tuesday that toxic matter recovered from 13 sites in Abidjan would be shipped to France for disposal.
"We believe that only through investigation of the ship and its logs can a chain of culpability be established"
Also on Tuesday night, protesters from the Greenpeace environmental group hooked themselves up to the ship's mooring lines to stop it leaving.
They were later arrested by border guards in Paldiski and fined.
Mike Townsley, a spokesman for Greenpeace, said: "We will not up anchor because we believe that only through investigation of the ship and its logs can the chain of culpability be established.
"[This is so that] what happened in Ivory Coast and the failure of the regulatory system can be fixed to guarantee that this never happens again."
Greenpeace has also filed suit in the Netherlands against Trafigura Beheer in another bid to ensure that the ship remains in Estonia.