The meeting is set to turn on new initiatives for getting the asylum process under control and and dealing with the critical situation on the Austrian border, where thousands of refugees are flocking into Germany on a daily basis.
At the same time Merkel pleaded for patience, saying that there were no quick fixes to the crisis, as thousands of refugees are still making their way across the Balkans towards Germany.
Seehofer had earlier demanded that the government change course before Sunday.
Merkel is now set to meet Seehofer, who is head of the Christian Social Union (CSU), sister party to Merkel's Christian Democratic Union (CDU) in Bavaria, on Saturday.
The Süddeutsche Zeitung reported on Wednesday that the pair will then meet with Social Democratic Party (SPD) head Sigmar Gabriel on Sunday.
Seehofer has described it as scandalous that Austria transports thousands of refugees through its country to the German border without the consent of Berlin.
Since the beginning of August at least 318,000 asylum seekers have arrived in Germany's south-eastern most state.
The Bavarian minister-president has constantly called for emergency measures to deal with the refugee influx, including setting a cap on the number Germany will let in and building reception centres at the border at which asylum cases would be initially reviewed.
He has gone as far as to threaten to take the federal government to the German constitutional court.
Berlin has however has been reluctant to criticize Austria, saying only that it has been in "constant contact" with Vienna throughout the crisis.