Europe’s attempts to deal with the unprecedented numbers of migrants arriving on its shores have fallen deeper into disarray after a raft of European Union countries unilaterally re-imposed border checks and the region’s justice ministers failed to agree on a plan.

Europe’s border-free travel area – known as the Schengen zone – appears to be disintegrating Monday as countries including Austria, Slovakia and Netherlands followed Germany’s lead by re-establishing temporary border controls in order to deal with thousands of migrants flowing through Europe.

Meanwhile, Hungary – a key conduit for migrants travelling north from southern Europe — has introduced strict migrant laws which allow the police to detain anyone attempting to breach a fence built on the border with Serbia.

Elsewhere, Czech Republic deployed more police to its border with Austria while France, Poland and Sweden said Monday they were monitoring the situation to see if border controls were needed.

Read MoreFour reasons why Europe’s migrant crisis matters

All those countries are members of the Schengen zone, in force since 1995, which allows passport-free movement of citizens between countries. The agreement does allow for temporary and «exceptional» border controls to be reinstated in cases of a «crisis situation.»

Geovien So | Pacific Press | LightRocket via Getty Images

Over the summer, Europe has seen thousands of refugees, mainly from war-torn Syria and Africa, arriving in the continent in search of a better life in Europe.

In a bid to find a comprehensive solution to the migrant crisis, justice and interior ministers from the European Union’s 28 members met in Brussels for talks on Monday. The discussions attempted to agree on a set of «emergency» measures on migration –including the relocation of 120,000 asylum seekers, on top of 40,000 agreed in July . However, the meeting failed to reach an agreement, with the prospects for progress looking dim.

In a statement issued after the meeting, the EU Council said the meeting merely agreed to «further develop resettlement possibilities» adding that only «some Member States committed to complete their pledges (to relocate 40,000 persons currently in Greece and Italy) already by the end of November.»

There also seemed to be no more progress h on the relocation of 120,000 people, which was proposed by European Council president Jean-Claude Juncker last week. In its Monday night statement, the Council said that while member states agreed «in principle» to relocating those additional migrants, more work needed to be done «on the preparation of a formal decision to implement this commitment.»

Read MoreMigrants could help solve Europe’s aging problem

In a nod to countries who say they will struggle to accept more migrants, the Council said it would also pay attention to the «flexibility that could be needed by member states in the implementation of the decision, in particular to accommodate the current situation and unforeseen developments.»

Quotas unworkable?

European governments have been mobilised to act by the sheer numbers of migrants arriving in the region, but policies on migration, asylum claims and repatriation of failed claimants appears to be far from effective or unified.

German Interior Minister Thomas de Maizière said on Tuesday that border controls were temporary but that Europe was a «way off solving the refugee crisis,» Reuters reported.

There is strong resistance from Romania, Hungary, Slovakia, Czech Republic and Poland to any compulsory measures to relocate refugees — although these countries receive far fewer asylum claims. Germany, on the other hand, is the most attractive place for migrants and it said on Monday that it expects 1 million migrants to arrive this year, revising an earlier expectation of 800,000.

Carsten Nickel, senior vice president of risk advisory Teneo Intelligence, said in a note Monday that «a mandatory quota for the EU-wide relocation of migrants is unlikely to be achieved quickly, if at all.»

«Any eventual agreement is unlikely to greatly involve the (European) Commission and will instead be reached between member states, ensuring the supremacy of capitals rather than EU institutions over this core issue of national sovereignty ,» he wrote.

‘It won’t be pretty’

Barring any emergency meeting of heads of state and government, Nickel thought interior ministers may come closer to a deal at their next meeting on October 8. Whether an agreement can be found that placates the former-Communist bloc in eastern Europe remains to be seen, however.

These «recalcitrant Europeans,» according to Ian Bremmer, president of political risk research firm Eurasia Group, will drive a hard bargain.

«The strongest opposition has come from eastern Europe…they have strong domestic resistance to accepting refugees, and see political benefits in taking a hard line against Germany. which means they’ll try and exact a pound of flesh on other issues…It won’t be pretty,» he warned in a note Monday.

Europe was less united than ever, and once again, as with the Greek financial crisis, it was cobbling together a short-term plan to deal with an «expanding» crisis, Bremmer added.

«It’s very much like the Greece (third bailout) deal — nothing more than a last minute, short-term patch that doesn’t resolve an expanding challenge. As an actor on the international stage, ‘Europe’ has less cohesive norms, values, and governance than at any time since the union was created,» he said.

– By CNBC’s Holly Ellyatt, follow her on Twitter @HollyEllyatt. Follow us on Twitter: @CNBCWorld




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