Slovakia is launching a legal challenge to mandatory quotas that were passed in a majority vote on Tuesday.
Meanwhile, Hungary's prime minister has proposed a radical budgetary revamp to raise funds.
The summit will focus on tightening EU borders and aiding neighbours of Syria, from where many migrants come.
The talks were continuing well into the night, having started just after 19:00 Brussels time (17:00 GMT).
Draft proposals seen by the BBC, that are being discussed at the summit, include:
European Council President Donald Tusk called for "a concrete plan" to secure the EU's external borders, "in place of the arguments and the chaos we have witnessed in the past weeks".
As she arrived at the summit, Lithuania's President Dalia Grybauskaite said it was "not a lack of European unity, but a lack of European wisdom" that had led to this point.
On arriving, British Prime Minister David Cameron said the UK would be giving another £100m ($152m) to help Syrian refugees, including £40m towards the World Food Programme.
"We need to do more to stabilise the countries and the regions from which these people are coming," he said.
The UK has opted against taking part in the relocation scheme and has its own plan to resettle migrants directly from Syrian refugee camps.
The scale of the problem was highlighted again on Wednesday when Croatia revealed that 44,000 migrants - including 8,750 on Tuesday - had arrived there since Hungary completed a fence along its border with Serbia last week.
Analysis: Chris Morris, BBC Europe correspondent
As thousands of people continue to arrive on European shores, EU leaders are trying to focus on longer term solutions, to try to stem the flow.
The EU can't ignore the divisions and disagreements that have emerged in the last few weeks between member states that have different ideas about how this crisis should be confronted.
One EU official said there was a need to clean up the bad blood around the table.
Progress may be made this evening, but it will take years of political engagement to make a significant difference. And there will be more bumps in the road.
Relocation deal explained
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One young Syrian's story
On Tuesday, in a rare move for an issue involving national sovereignty, EU interior ministers approved the resettlement scheme by majority vote rather than unanimous approval.
The deal will see thousands of migrants moved from Italy and Greece to other EU countries. A proposal to take 54,000 migrants from Hungary was dropped.
The plan's opponents have lashed out.
However, Czech PM Bohuslav Sobotka said on Wednesday it would not launch a court challenge, adding: "Europe must not fall apart on the migration crisis."
Romania said it could manage its allocation but President Klaus Iohannis insisted mandatory quotas were not the answer.
The UN has warned that the relocation alone would not be enough to stabilise the situation.
Close to 480,000 migrants have arrived in Europe by sea this year, and are now reaching European shores at a rate of nearly 6,000 a day.
Austrian police told the BBC at least 7,000 people arrived from Hungary on Wednesday.
Source: European Commission
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EU migration: Crisis in graphics
A note on terminology: The BBC uses the term migrant to refer to all people on the move who have yet to complete the legal process of claiming asylum. This group includes people fleeing war-torn countries such as Syria, who are likely to be granted refugee status, as well as people who are seeking jobs and better lives, who governments are likely to rule are economic migrants.
Splits within the EU on the relocation of 120,000 migrants have been further exposed as leaders hold an emergency meeting in Brussels.