In an impassioned appeal on Wednesday at the European Parliament in Strasbourg, France, Juncker unveiled a list of new proposals to help Europe confront its biggest refugee crisis since World War II.
The plan, which will see Germany and France take in the lion's share of refugees, is likely to run into serious resistance from some member states.
Juncker warned that Greece, Italy and Hungary, where most of the refugees are currently camped out, can no longer cope alone.
"It is time for bold, determined action by the European Union," Juncker told EU lawmakers, noting that some 500,000 migrants have entered Europe this year, many from conflict-torn Syria and Libya.
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In his proposal, Juncker wants 22 of the member states to accept another 120,000 people, on top of the 40,000 already agreed upon in June, bringing the total number to 160,000.
All the 120,000 additional refugees are currently in Greece, Italy and Hungary. Under the new proposal Germany will take in 31,443 refugees; France, 24,031; Spain, 14,931; Poland, 9,287; and The Netherlands, 7,214. Other member nations will take the rest based on wealth, population, unemployment rate and the number of asylum applicants already processed.
"It is a matter of humanity and human dignity," Juncker said.
"We are fighting against Islamic State, why are we not ready to accept those who are fleeing Islamic State?" he said, referring to the Islamic State of Iraq and the Levant (ISIL) armed group that has taken over territories in Iraq and Syria.
"It is high time to act, to manage the refugee crisis, because there is no alternative. No rhetoric. Action is what is needed for the time."
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Al Jazeera's Jacky Rowland, reporting from Strasbourg, said Juncker "told it like it is", making the point that many Europeans themselves have been refugees not long ago.
Stiff resistance
Under the proposal, countries refusing to take in refugees could face financial penalties.
Germany, which hosts the largest number of refugees, has already backed the idea. It has welcomed Syrian refugees, waiving EU rules and saying it expects to deal with more than 800,000 asylum seekers this year alone.
Italy, which is one of the main arrival points for thousands of refugees crossing the Mediterranean is also in favour and so are France and Spain.
But the plan has met stiff opposition from countries like Hungary, which is building a fence to keep refugees away from its borders.
Al Jazeera's Mohammed Jamjoom, reporting from the Roszke on the Hungarian Serbian border on Wednesday, said Hungary has already clamped down on refugees crossing the country, and has stopped providing information to countries like Austria about the movement of refugees.
Its neighbours, the Czech Republic, Poland and the Slovak Republic have also said that mandatory and permanent quotas would be unacceptable.
Following Juncker's speech on Wednesday, Czech Prime Minister Bohuslav Sobotka said Europe does not need a new plan to deal with the crisis, and instead stick to an earlier agreement.
"It is necessary to move from negotiating tables to action and to work hard on those measures that we have approved with other EU leaders and agreed on in the past months," Sobotka said in a statement.
The EU's first refugee plan never won full support, and only around 32,000 refugees have been allocated. Hungary was among the countries to reject it, along with the Czech Republic, Slovakia and Poland.
Juncker wants both plans endorsed on Monday at a meeting of EU interior ministers in Brussels. "This has to be done in a compulsory way," he said.
In Berlin, German Chancellor Angela Merkel backed the new plan and also called for it to be made compulsory.
On Monday, France threw its weight behind the EU plan by saying that it would take in 24,000 refugees this year, exactly the figure the new scheme calls for.
Britain, which is not taking part, announced separately that it would welcome up to 20,000 refugees currently in countries outside of the EU over the next five years.
On Wednesday, the Commission also unveiled a plan to set up a $2bn fund to help African nations better manage their borders and help reduce the number of refugees heading for Europe.
Source: Al Jazeera and agencies
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