Merkel said people would be kept in the new centers for 48 hours at most.
Austria's right-wing Chancellor Sebastian Kurz, who is closer to Mr Seehofer than to Mrs Merkel on the migrant question, said "we have full confidence in Seehofer's words yesterday".
Merkel said that securing the external borders of the European Union is not the creation of a "fortress against the people, brought by the smugglers".
However, differences remain over its implementation.
"I believe the soul of Europe is humanity and if we want to retain this soul and play a role in Europe with these values then Europe can't simply decouple from the need and suffering". She said Germany was delighted that the English soccer team was still in the World Cup competition in Russian Federation.
The FT said that three diplomats said the European Commission was studying whether it would be feasible to negotiate a deal with other big vehicle exporters such as the US, South Korea and Japan.
Media captionWhy is the Aquarius migrant rescue ship empty?
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.
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Seehofer, whose threat to leave his post as interior minister put the future of Merkel's government in jeopardy, appeared satisfied with the deal.
But this is also causing some disagreement.
Germany, Austria and Italy will hold talks next week on how to "shut" the southern migration route into Europe and plan to work together on that issue, Germany's Interior Minister Horst Seehofer said on Thursday.
"Before taking back not one asylum-seeker in Italy, we'll wait until the other countries take the tens of thousands who should have been already taken with the relocation" accords, Salvini told reporters in Rome.
"We think that the people Germany is sending back must go to Greece and not Hungary".
"You know that our coalition partner has problems with the term transit centers", said Seehofer, "that's why they prefer to talk about transit procedures in police facilities, and that expresses what we do in the future".
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. If this did not occur, between 4,000 and 5,000 people per day would enter Germany.
About 56,000 migrants have arrived in Europe so far this year, the International Organization for Migration says.