The commission has announced that it expects member states to relocate 40,000 Syrian and Eritrean nationals who entered Greece or Italy after 15 April, over a period of two years.
Member states will receive €6000 for each person they relocate on their territory.
Germany, France and Spain have been asked by the commission to welcome the largest portion of these 40,000 migrants, with figures based on countries' total population, GDP, average number of asylum applications and unemployment rates.
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Germany would take in 8763 (21.91 per cent) refugees, 6752 (16.88 per cent) for France and 4288 (10.72 per cent) for Spain.
These are not binding quotas, as member states will be free to decide how many people they grant refugee status to, but before this can happen, the plans must be approved by the European parliament and national governments.
While MEPs have welcomed the proposals, they did have some reservations, with parliament's EPP group vice-coordinator in the civil liberties, justice and home affairs committee Roberta Metsola stressing that they "must go hand in hand with other measures".
"This is the first step and should be followed by a permanent system", she underlined.
She added that this was "an emergency response to an emergency situation in Italy and Greece. It is an acknowledgement that this is a European challenge that deserves a European response by every member state, acting in solidarity."
But with three member states expected to welcome half the refugees, and two - the UK and Denmark - already opting out of the scheme, there is little indication of any solidarity between EU countries.
Birgit Sippel, parliament's S&D group spokesperson for the civil liberties, justice and home affairs committee, said, "we have been talking about this issue for too long; now is the time to act and put the lives of asylum seekers ahead of national egos".
She called for "a permanent relocation mechanism that distributes asylum seekers equally across all member states".
However, the German deputy did commend the commission for having "finally shown some backbone on the issue", explaining that "it is high time that we have a fair way of distributing asylum seekers between member states".
ECR group home affairs spokesperson Timothy Kirkhope was sceptical of the proposal, accusing the commission of having "resigned themselves to dealing with the symptoms rather than the cause".
In his view, "while there is political unrest and war in north Africa and the Middle East, the numbers arriving in Europe are not going to reduce unless we tackle the problem at the source".
The British MEP urged the commission to "address how to stop trafficked vessels from setting sail in the first place by helping to create stability and safety in these war-torn countries".
Parliament's Greens/EFA group also had a mixed reaction to the proposed plans, with migration spokesperson Bodil Ceballos saying, "it is welcome that the commission is trying to corral EU governments into accepting their collective responsibility for refugees entering Europe."
"While a distribution system for handling asylum applications would be on element of this, it is in itself no panacea for a holistic and comprehensive asylum policy".
The Swedish deputy cautioned, "it is clear that a number of EU governments are opposed to this approach, so it remains to be seen what happens to these modest proposals".
She concluded, "the EU has a moral duty to do more to address the asylum crisis and this implies ensuring more opportunities for legal access and greater commitment on combating the underlying reasons why refugees flee their country of origin. The EU has to stop seeing those coming here as a threat".