“The talks are proceeding in a good climate,” Seehofer told public broadcaster ARD.
“But in the end, the heads of government may have to talk with each other again because of the complexity” of the matter, he added, as well as saying he wanted “clarity” in the coming days about whether an agreement could be struck.
Little concrete progress has been made since a crunch EU summit in July; while Greece has signalled a willingness to take back some migrants, Italy's right-wing government is more resistent.
Italian Interior Minister Matteo Salvini, the leader of the far-right League party, has said his country expects to see more action to toughen the EU's external frontiers before agreeing to any migrant return deal.
Greece and Italy, who have borne the brunt of migrant arrivals in recent years, are also insisting that in return for taking back certain asylum-seekers, Germany should take in others.
But Seehofer stressed that the number of returns must not outweigh the number of new migrants taken in.
“We can't sign up to that, the German people wouldn't understand if we took in more refugees than we sent back,” he told ARD.
Former Bavarian premier Seehofer has long been one of the fiercest critics of German Chancellor Angela Merkel's decision to open the country's borders to those fleeing conflict, persecution and poverty at the height of the migrant crisis in 2015.
Germany has since taken in over a million asylum-seekers, fuelling the rise of the far-right, anti-immigrant Alternative for Germany (AfD) party.
Seehofer, who heads Merkel's more traditional CSU sister party, recently threatened to turn back migrants at Germany's borders if they had already made asylum requests in other EU countries.
Fearing the domino-effect such unilateral action would unleash, Merkel instead pushed for a wider European Union response that includes migrant return deals with frontline states like Greece and Italy. Now, Seehofer has threatened to press on with his plans if no bilateral agreements are in place by early August.