Results on Monday showed the vote was marked by mass abstentions and protest votes on domestic issues.
As counting in the biggest transnational election in history neared a finish, the scale of public alienation highlighted challenges facing EU leaders when they meet later this week to try to finalise a first constitution for the bloc.
"Across Europe we have seen sitting governments receive significant protest votes against them," British Foreign Secretary Jack Straw said before starting a final round of pre-summit constitution negotiations in Luxembourg.
"One clear message is that voters across Europe, including in the United Kingdom, want a European Union that works better in their interests. That's the purpose of the draft constitutional treaty," he said.
But the huge protest vote against British Prime Minister Tony Blair's Labour Party, and gains for Eurosceptics in Poland, the Czech Republic and Sweden, raised doubts about whether the new charter will ever be ratified.
Britain is fighting to preserve national vetoes in core areas while Poland, the biggest of 10 new members, is resisting a change in the EU voting system that would diminish its power.
A mere 45.3% of nearly 350 million eligible voters bothered to cast ballots in the four-day exercise in cross-border democracy, the lowest turnout since direct elections for the Strasbourg-based assembly began in 1979.
The most startling figure was that participation in the EU's 10 new, mainly ex-communist east European member states was just 26%. Parliament spokesman David Harley called it a "disappointing and pathetically low turnout".
The European Commission said the main reason was that the European Parliament had too little power, while Estonian Foreign Minister Kristiina Ojuland said it showed that neither old nor new EU citizens understood the legislature's growing role.
"Across Europe we have seen sitting governments receive significant protest votes against them. One clear message is that voters across Europe, including in the United Kingdom, want a European Union that works better in their interests"
UK foreign secretary
For some, the low poll could undermine the assembly's legitimacy. "Of course I would have appreciated it very much if we had a stronger legitimation of parliament," German Foreign Minister Joschka Fischer lamented.
British voters punished Blair for his role in the US-led Iraq war and governing parties in France, Germany and Poland for economic stagnation, unemployment and painful social reforms.
Only the recently elected Spanish and Greek governments escaped public wrath, amplifying their recent national victories, as did Slovakia's centre-right coalition on a pitiful 17% turnout - the lowest in the 25-nation bloc.
Britain and Poland sent strident new voices of hostility to European integration to the EU legislature.
The UK Independence Party, which won its first three seats in 1999, grabbed 12 this time, while opposition parties in Poland, including the populist Self Defence and the League of Catholic Families, beat the ruling Socialists into fourth place.
The overall balance in the European Parliament, which has growing powers over EU spending, financial regulation, food safety and environmental rules, was little changed.
The centre-right European People's Party was set to remain the biggest group with 272 of the 732 seats, the Socialists came second with 200, the Liberals third with 67 and the Greens fourth with 42.
Politicians said the Socialists and an augmented Liberal group that may be boosted by pro-integration defectors from the EPP could form an alliance to dominate the new parliament, possibly in a "rainbow coalition" with the Greens.
Liberal leader Graham Watson said he was talking to French centrist UDF leader Francois Bayrou, whose 10 deputies may quit the EPP, and European Commission President Romano Prodi, whose Italian centre-left followers straddle all three groups.
"We retain our pivotal role in the balance of power in the new house," he said, adding that his aim was "to fight the tired scepticism of the right wing".
Polling was marked by apathy
However, a return to the traditional power-sharing between EPP and Socialists which prevailed until 1999 is also possible.
Parliament will also have a say in the choice of European Commission president by EU leaders in Brussels on Thursday and Friday, since it must approve their choice in a vote on 21 July.
A centre-left alliance could improve the chances of Belgian Prime Minister Guy Verhofstadt, the front-runner, although he faces opposition from Britain, Nordic and east European states.
There is wide support among EU leaders for Luxembourg Prime Minister Jean-Claude Juncker, a Christian Democrat triumphally re-elected as the EU's longest-serving head of government on Sunday.
But he has vowed to stay in the 450,000-strong Grand Duchy rather than serve 450 million Europeans in the EU's hot seat.