At their plenary session in Strasbourg, MEPs adopted the new directive by 588 votes in favour and 42 against, amid three abstentions.
The directive introduces compulsory criminal sanctions for serious cases of maritime pollution, and also forces member states to impose stringent penalties for minor cases if they are repeated, deliberately caused or the result of serious negligence.
The EU law leaves it to national governments to set the penalties, but requires them to be "effective and dissuasive", not only for ship-owners but also for the "other agents" involved in sea transport, such as cargo owners.
"Repeated minor discharges made with intent, recklessly, or due to serious negligence must be considered criminal offences and punished with effective, proportionate and dissuasive penalties," the Parliament said in a statement released after the vote.
MEPs reached a first-reading agreement with the 27 EU member states last week, paving the way for a swift adoption of the rules, it added.
Following the vote, Luis de Grandes Pascual, a Spanish centre-right MEP (EPP-ED) who steered the proposal through the EU assembly, said Europe had "made a big step forward to stop maritime pollution".
"For the first time, we will have compulsory criminal penalties for all the responsible parties in the maritime sector," he said.
Pascual explained that until now it has been "cheaper" for large shipping companies to pay fines rather than implement laws to prevent pollution. "This directive will help remove this unwelcome laissez-faire attitude towards pollution law from the maritime industry," he said.
The directive is a revised version of a text initially tabled by the Commission in February 2007. The original proposal had to be modified following a European Court of Justice (ECJ) ruling later that year.
The ECJ ruling, issued on 23 October 2007, supported the EU executive's proposal to impose criminal sanctions for pollution at sea. But it also stated that it does not have the authority to lay down the type and level of criminal penalty, which is left to the discretion of member states (EurActiv 24/10/07).