"The threat posed by right-wing anti-semitism and terrorism is elevated in Germany," Seehofer said on ZDF public television.
This means such an attack could happen "at any moment," he added.
Seehofer said there are an estimated 24,000 far right extremists in Germany. He added that half of them are considered potentially violent with "a very high affinity for firearms."
Seehofer's warning came two days after Stephan Balliet, a 27-year-old loner, was arrested for killing two people after trying to gain entry to a synagogue in the eastern town of Halle where dozens of worshippers were marking Yom Kippur.
Though he failed to batter his way into the building, the assailant, armed with four apparently home-made rifles and grenades, killed a female passer-by and then shot dead a man who tried to take refuge in a kebab restaurant.
Police eventually captured Balliet -- who had four kilos (nine pounds) of explosives in his car -- after a gun battle that left him wounded.
Earlier Friday, a spokesman for the federal prosecutor's office in Karlsruhe said Balliet had confessed to the assault and confirmed ”far-right and anti-Semitic motives."
Given the range of weapons he had on his person, the death toll could have been far higher had Balliet managed to force his way inside the synagogue.
He filmed and live-streamed the 35-minute assault as he raved at Jews and denied the Holocaust. He also published an online manifesto expressing anti-Semitic sentiments.
"This manifesto appeared on the internet the day after his act," said Seehofer, who added that synagogues and other Jewish venues would in future be better protected.
The minister announced the creation of new security service posts to that end and added that the government would swiftly enact a ban on six small far right groups.
"We are extremely alert on this matter," he insisted.