Merkel's Christian Democratic Union (CDU) passed a resolution on Sunday night supporting her position on migration.
He told Sky News: "The problem is, the agreement only exists between the CSU, Seehofer's party and Angela Merkel's CDU".
The flashpoint issue was Seehofer's demand to order German border police to immediately turn back all asylum seekers already registered elsewhere in the European Union, and his threat to do so against Merkel's wishes.
Some Social Democrats accuse the CSU of wanting to appear tough on immigration before a regional election in Bavaria in October where the conservatives are expected to lose voters to the anti-immigrant party Alternative for Germany.
Following marathon talks at the Brussels summer summit, European leaders eventually reached a compromise on migration in the early hours of Friday.
"I would like very much for the CDU and CSU to continue working together", Merkel said, admitting she had made concessions to Seehofer's demands, public broadcaster Deutsche Wellereported.
Merkel, Seehofer, Nahles and senior members of their parties met in the chancellery on Tuesday evening to discuss the plan.
Seehofer, a long-time Merkel critic, had openly challenged her with a plan to order border police to unilaterally shutter German border crossings with Austria to many asylum seekers, effectively daring the chancellor to fire him.
"In this case, the CSU, Seehofer's party, would quit the coalition government", he continues.
Merkel, who has been in office since 2005, warned last week the battle over migration could decide the EU's future.
Seehofer had initially proposed an immediate rejection of immigrants who have been registered in other European Union countries but later agreed to a phased implementation of the plan, contradicting Merkel's stance on the matter.
The document also outlined deals with 16 other countries to return already-registered migrants if they reached Germany.
Ms. Merkel, anxious about European Union unity, opposes such a unilateral move without agreements between Germany and its neighbors.
As he entered a CDU crisis meeting yesterday, deputy leader Armin Laschet said the sister parties "want to hold onto" their alliance.
The "Free State" with its beer-and-lederhosen Alpine traditions, powerful industries and impenetrable dialect has a more conservative bent than other German regions.
Ahead of a hard Bavarian state election in October, the CSU is determined to show it is tough on migration. "I have not studied it in detail but at first glance - and I have asked the legal services to look at it - it seems to me to be in line with the law", Juncker told a news conference in Strasbourg.
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Gelson Martins and Raphael Guerreiro are both in contention to start having returned to full training following injuries. The French defeated Argentina 4-3 earlier on Saturday. "Even if he scores three goals , he has a team working for him".