At the plenary in Strasbourg on Wednesday, they voted against the list, which had been drawn up by the European Commission, by 392 votes to 80, with 207 abstentions.
Earlier this year, Parliament vetoed a similar list drafted the Commission, of countries thought to be at risk of money laundering, financing terrorism or promoting tax evasion.
A resolution voted on Wednesday says the EU should have an "independent, autonomous process for judging whether countries pose a threat of financial criminality rather than relying on the judgement of an external body."
The list of third-countries judged by the Commission to have "strategic deficiencies" in their anti-money laundering and countering the financing of terrorism regimes are: Afghanistan, Bosnia and Herzegovina, Guyana, Iraq, Lao PDR, Syria, Uganda, Vanuatu, Yemen, Iran and Democratic People's Republic of Korea (DPRK).
Under the EU's anti-money laundering directive, the Commission is responsible for producing an inventory of countries thought to be at risk of money laundering, tax evasion and terrorism financing.
People and legal entities from blacklisted countries face tougher than usual checks when doing business in the EU.
Currently, the Commission relies heavily on the international body, the financial action task force (FATF) in drawing up its list.
Judith Sargentini, Parliament's co-rapporteur on the anti-money laundering directive, told this website, "The European Commission needs to take its role in tackling money-laundering much more seriously.
Having had their proposals rejected the first time round, they have made only the most cosmetic of changes. It stretches credibility to breaking point for the Commission to suggest that the absence of one country was the only flaw in the previous text.
"It is of utmost importance that member states are able to collect taxes and not have them lost via opaque constructions in tax havens. An ambitious list would contribute to tackling money-laundering and combatting tax evasion. We now ask once again that the Commission conducts a thorough assessment and return with a list that is fit for purpose."
Sven Giegold, financial and economic policy spokesperson of the Greens/EFA group, said, "It beggars belief for the Commission to present a list that includes none of the world's famous tax havens. Faced with the recent leaks on money laundering and tax evasion, it is unacceptable that Panama and other important tax havens are still not included on the Commission's blacklist.
"The Commission cannot possibly hope to beat money laundering with the resources it is currently dedicating to the task. To win the fight against money laundering and terrorist financing, the Commission will need to invest much more, especially in human resources."
Giegold, who sits on the special committee set up by Parliament to investigate tax havens, told this website, "The net benefits, to the public purse and in tackling organised crime, will be more than worth the investment."