The German Chancellor said it was “not acceptable” for EU members to shirk their responsibility to meet migrant quotas.
Concerns about migration have overshadowed the European Council summit in Brussels, which had been expected to revolve around Brexit and eurozone reform.
Speaking on the second day of the EU summit, Angela Merkel said: “We are not so in agreement as regards internal solidarity on the migration issue. In most areas, if not all areas, we show solidarity, as part of the EU.
“But there are some areas where solidarity is not shown and that is something I find not acceptable.”
Angela Merkel, whose arrival in Brussels yesterday provided a brief respite from her domestic political woes, said there “cannot be selective solidarity among EU member states”.
Germany gave refuge to more than one million asylum seekers in 2015 and has been championing the policy of sharing refugees through quotas, when numbers could overwhelm other countries.
Bitter infighting erupted within the EU this week when Mr Tusk unveiled his plans to relocate refugees.
It exposed the deep divisions within the EU as to how to deal with the fallout from the aftermath of the 2015 migration crisis.
Mr Tusk sent a note to all the EU leaders which stated: “Only member states are able to tackle the migration crisis effectively. The EU’s role is to offer its full support in all possible ways,” adding “the issue of mandatory quotas has proven to be highly divisive and the approach has turned out to be ineffective.”
Several countries reacted angrily to the comments and his implication that the primary responsibility for the refugees should fall on the frontline countries such as Italy, Spain and Greece.
Later in the day, Mr Tusk was forced into a humiliating climbdown later in the day due to the pressure and issued a revised note which called for the EU institutions to work together with individual countries over migration issues.
Mr Tusk wrote: “The EU can only tackle illegal migration effectively with the full involvement of Member States and by the coordinated use of EU and Member States means and instruments.
“No Member State can deal with this common challenge on its own, but decisive action by lead Member States, backed by the EU and assistance from other Member States, has proven to be effective.”
On the first day of the EU summit on Thursday, Mr Tusk begged members to unite against the challenges faced by the EU.
He said the Brussels club can only overcome major obstacles with unity.
As he arrived for a meeting with Visegrad leaders ahead of the EU Council, he said: “We will deal with the issue of a lack of unity which is very visible – I am talking about the EMU and migration.
“When it comes to EMU the divide is between North and South when it comes to migration it is between East and West.
“These divisions are compounded by emotions it makes it hard to find even common language and rational argument for this debate.
“This is why we should work on our unity than ever before.”
On the other side of the debate, the Visegrad group (V4) – made up of Poland, Hungary, Slovakia and the Czech Republic – has come out in support of Tusk’s comments.