The compromise comes after lawmakers from both conservative parties in the German coalition urged the Chancellor and her interior minister on Monday to resolve the dispute over migrant policy that has thrown her three-month-old government into disarray. The German leader would not comment Sunday on the outcome of the talks.
Weeks of "Merkel-bashing", however, have failed to help the CSU, as a Forsa poll last week showed around 68 percent of Bavarians backed Merkel's quest for a Europe-wide answer to migration rather than Germany going it alone.
Late on Sunday, Mrs Merkel's Christian Democratic Union (CDU) passed a resolution supporting her position on migration.
But the more conservative CSU anxious its credibility was at stake as it tries to curb support for the rival anti-migration Alternative for Germany party, known as the AfD, in the Bavarian election.
Earlier this week, EU leaders hammered out a deal to share out refugees on a voluntary basis and create "controlled centres" inside the European Union to process asylum requests.
However, Mr Seehofer apparently does not agree.
Nevertheless, the anti-refugee, anti-Islam Alternative for Germany (AfD) was propelled into federal parliament for the first time past year by outrage over immigration, leading to months of paralysis while Merkel struggled to find a workable coalition.
"We can achieve a lot in a government, but not outside", Soeder said.
"It is also sustainable and in accordance with the European ideal".
"I think it's caused by the atmosphere with the AfD", said Joerg Hauvede, 47, as he left Berlin's main train station.
But the divisions within the German government over the issue are also being played out in other European Union countries, and this was reflected in the vague wording of Friday's deal.
"Germany has not addressed us and I will not sign this agreement", Czech Prime Minister Andrej Babis said in a statement.
In an extremely fluid situation, Merkel and Seehofer are due to meet later in the day and before that, a joint session of the parliamentary groups of the CSU and CDU is due to take place, although there was some doubt if it would go ahead.
"It goes absolutely in the right direction", he said but added he would keep up the pressure to obtain more clarity on the details.
"I understand that this is a dramatic attempt to save her own position, but absolutely there is no agreement", Jacek Sasin, a senior Polish government official said, on public television on Sunday.
Seehofer, whose party faces a state election in the fall, has threatened to turn away at the borders migrants whose asylum requests Germany already rejected or who already sought asylum elsewhere in Europe.
The CSU's discontent comes despite many of its longstanding migration demands appearing in the European Union summit deal.
"We should convene a #Migration Summit of federal, state and local governments and all governmental parties, " he said on Twitter.