Horst Seehofer, leader of the Bavarian sister party the CSU, criticised the EU for its “moralising” tone towards eastern countries, like Hungary and Poland, who have refused to take in migrants under the bloc’s quota system.
Mr Seehofer said the attitude was “counter-productive”, adding: “Every country has its pride”.
The conservative politician, a critic of Angela Merkel’s 2015 migrant policy, urged the EU to stop making decisions “over the heads” of member states.
He told German Sunday newspaper Die Welt am Sonntag: “The EU commission is often patronising.
“We need to put more energy into dialogue on the distribution of refugees. If we keep negotiating patiently, a majority of countries will support it.”
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Mr Seehofer said other countries could contribute in other ways, perhaps by sending more personnel to the EU borders, or by contributing more for joint border patrols.
The EU has long struggled to get a grip on controlling the chaotic migrant crisis as members turn their backs on the issue.
His remarks against the EU could exacerbate tensions in the uneasy new “grand coalition” between Merkel’s conservatives and the centre-left Social Democrats.
Mr Seehofer has already announced a “master plan” to kick rejected immigrants out of Germany at a faster rate under the new coalition government.
He has vowed to “get tougher” on those who break the law in Germany or are deemed a security threat as he said repatriations and deportations must be “raised significantly”.
Mrs Merkel faced an uphill struggle to cling on to her fourth term in power after their stance on immigration saw her party lose swathes of votes to the far-right Alternative for Germany (AfD) at the German elections.
She welcomed more than one million refugees into Germany as part of her widely-criticised open door refugee policy.
In 2015, the EU saw a huge spike in the number of people applying for asylum as hundreds of thousands of people arrived after fleeing conflict in the Middle East and Africa.
In response to the increase, Mrs Merkel agreed to accept more than one million refugees into Germany.