Juncker's plans were set out in a "state of the union" annual address in which he outlined the priorities of the European Commission, the BBC has reported.
He opened his speech by admitting the European Union was "not in a good situation... There is a lack of Europe in this union, and a lack of union in this union."
He said tackling the crisis was "a matter of humanity and human dignity".
Juncker's proposals are the following: EU member states should accept their share of an additional 120,000 refugees, building upon proposed quotas to relocate 40,000 refugees which were set out in May (though governments then only actually agreed to take 32,000);a permanent relocation system to "deal with crisis situations more swiftly in the future"; efforts to strengthen the EU's common asylum system; a review of the so-called Dublin system, which states that people must claim asylum in the state where they first enter the EU.
"It's 160,000 refugees in total that Europeans have to take into their arms and I really hope that this time everyone will be on board - no rhetoric, action is what is needed," he told MEPs.
The proposals will be discussed by EU home affairs ministers on 14 September in Brussels.
The new plans - for an extra 120,000 migrants - would relocate 60% of those now in Italy, Greece and Hungary to Germany, France and Spain.
The numbers distributed to each country would depend on GDP, population, unemployment rate and asylum applications already processed.
Countries refusing to take in migrants could face financial penalties.
Germany, the main destination for many migrants, supports quotas, but the Czech Republic, Slovakia, Poland and Romania have opposed the idea of mandatory quotas.
