Altmaier told ZDF public television on Friday that Merkel was being "constantly briefed" on developments in the southern city, where police say up to three gunmen are still at large.
"The cabinet ministers concerned are on their way to Berlin," he added.
German Interior Minister Thomas de Maiziere interrupted his holiday after the shooting occurred and is returning home.
According to Munich police, on Friday, at least eight people were killed in a shooting at the Olympia shopping center in the German city of Munich.
Another body was found not far from the site of the shooting and police are investigating whether it could be that of one of the attackers.
German Foreign Minister Frank-Walter Steinmeier said that there is contradictory evidence about the Munich attack and the motive has not been determined.
A special operation is underway to capture the shooters.
According to the German Bild newspaper, German nationals dissatisfied with the migration policy could have been involved in the attack, as one of the videos of the shooting captures a man shouting "I am German."