The incident happened in Souda port on the island of Crete
. Two of the victims drowned while the third died from hypothermia. A further 16 people were missing.
About 50 evacuees used a rope to descend from the ship which had already moored at the port to enter Greece illegally, the Civil Protection ministry said in a statement.
The victims, all from Bangladesh
, probably tried to avoid being sent back to their home country, according to a coastguard official.
A total of 29 people were hospitalized. Divers were searching the Souda harbor for the missing. A coastguard official said, however, that they might have made it to the shore, escaping inland.
The "Ionian King," a ferry, was carrying a total of 1,288 evacuees from Tripoli, most of them Bangladeshis.
The unrest has heightened worries about a wave of illegal immigration into Europe. Thousands of workers from countries such as Vietnam and China have been evacuated from Libya
, many of them on Greek ships.