Seehofer planned later on Thursday to hold talks in Vienna with Austrian Chancellor Sebastian Kurz, who has said his government would take measures to protect its southern borders - including with Italy where many migrants first set foot on European Union soil - if Germany proceeded with the transit zones.
She backed a wider but later-aborted proposal for border facilities over two years ago.
SPD leader Andrea Nahles also said there would be no unilateral action concerning migration, but that there would be quicker processes for handling asylum applications according to the Dublin rules.
In response, Austrian Chancellor Kurz said on Tuesday that he would not accept a plan that is disadvantageous to his country, indicating he will seek stricter border controls if Germany implements the agreement.
Seehofer also announced that he will meet next week with his Italian and Austrian counterparts for talks aimed at restricting the Mediterranean sea route used by migrants heading to western Europe.
Merkel made the remarks at a joint press conference after a meeting with the visiting Hungarian Prime Minister Viktor Orban. "I am confident that we will reach an agreement with the SPD as well", Seehofer said.
Seehofer, whose hard line on immigration has prompted weeks of conflict with the chancellor, promised that Germany would not send asylum seekers to Austria if they were turned away at the German border, although details remained unclear.
Germany's Social Democrats (SPD) has reached an agreement on migration with the other parties in Chancellor Angela Merkel's coalition, its head said on Thursday, stressing that there would be no transit centres of any kind.
Influential news weekly Der Spiegel said Thursday that the hard-fought compromise marked an "Orbanisation" of Merkel's policies. Such a move, it said, could address Mr Trump's complaint that the U.S. sector is unfairly treated, while reducing export costs for other participating countries' auto sectors.
According to an industry source, the USA ambassador to Germany told German vehicle bosses from BMW, Daimler and Volkswagen at a meeting on Wednesday that Trump could abandon such threats if the European Union scrapped duties on US cars imported into the bloc. Kurz indicated it would not be possible to push the idea of camps in non-EU countries during the next six months.
He added that before any asylum-seekers are returned to Italy, "we want clear commitments on men, means and money to protect the external borders" of the EU. And there is only one solution: closing off of the borders, and bringing the support over there.