In a short statement, which EU diplomats said was intended to increase pressure on Israel after last month's killing, EU foreign ministers said the assassination raised "profoundly disturbing" issues and said citizens' rights were violated.
Dubai has accused Israel of involvement in the killing of Hamas commander Mahmoud al-Mabhouh in a hotel in Dubai last month. Israel has declined to confirm or deny it had any role.
"The EU strongly condemns the fact that those involved in this action (the assassination) used fraudulent EU member states' passports and credit cards acquired through the theft of EU citizens' identities," the ministers said in a declaration agreed at talks in Brussels.
"The EU welcomes the investigation by the Dubai authorities and calls on all countries to cooperate with it."
Diplomats said no direct reference was made to Israel in the statement because there was no proof Israeli agents carried out the assassination.
"I don't want to put forward allegations against Israel -- on what basis can I do that?" Austria's foreign minister, Michael Spindelegger said.
"I see no context that it really was an assassination and that the Israeli government is involved -- all those are assumptions but there are no proofs."
Dubai authorities say at least 11 assassins travelled on forged British, Irish, French and German passports to carry out the killing on the orders of Israel's spy agency Mossad.
Mabhouh was involved in smuggling weapons from Iran to the Gaza Strip, the Hamas militant group has said.
'Rigorous and legal document'
The EU declaration represents a ramping up of diplomatic pressure on Israel over the killing, but is unlikely to have any long-term repercussions for EU-Israeli ties. Israeli officials have played down the possibility of a full-blown crisis.
Israeli Foreign Minister Avigdor Lieberman was due to meet a number of EU foreign ministers on the sidelines of Monday's meeting.
After meeting Ireland's foreign minister, Lieberman issued a statement saying he had responded to a question about "the death of the terrorist Mabhouh" by saying "there is no information showing that Israel is involved in the matter".
A spokesman for Hamas said the statement lacked teeth.
"Condemning the use of (European) passports was insufficient. The statement did not indicate any condemnation of the crime, Mabhouh's assassination," Hamas spokesman Sami Abu Zuhri said in Gaza.
"This will tempt the occupation to carry out more crimes of this kind," he said, using the militant group's term for Israel.
France and Germany have asked Israel for an explanation, but the French and German foreign ministers were not scheduled to attend Monday's foreign ministers' meeting.
Britain wants Israel to cooperate fully as it carries out its own investigation into how as many as six British passports could have been forged and used by assassins to enter Dubai before killing Mabhouh in a hotel room on Jan. 19.
Spanish Foreign Minister Miguel Angel Moratinos, whose country holds the EU presidency until the end of June, said the falsification of the documents was a problem for all EU states.
"We're extremely concerned that a passport, which is a very rigorous and legal document, can be used in a different manner and for a different purpose," he told reporters in Brussels ahead of the foreign ministers' meeting.
Keeping its policy of ambiguity on intelligence issues, Israel has said there is no proof that it killed Mabhouh. Hamas is shunned by the West for rejecting its calls to recognise Israel and renounce violence.
Israel's deputy prime minister said on Sunday there was more to the incident than met the eye and that Israel's ties with Europe were good.
Dubai police say they are virtually certain Israeli agents carried out the killing and have released the identities of 11 people using European passports who they say were involved.
Six Britons with the same names of members of the alleged hit team live in Israel and said they were victims of identity theft. The information raised speculation that the Mossad copied their passports and amended the documents to allow the assassins to enter the Emirate, which has no diplomatic ties with Israel.