Policemen climb over a wall of the Jewish cemetery close to the site of a shooting in Halle an der Saale.
Police later said they arrested one person, though an earlier tweet suggested there may have been multiple "perpetrators" who fired "several shots".
One person is believed to have been arrested. Jewish people observing the holiday will fast from sundown on Tuesday until sundown on Wednesday and spend the majority of the day in synagogue engaged in prayer. "But the door remained closed - God protected us".
Two people also suffered serious bullet wounds in the attack and were being operated on, a spokesman for the city's hospital said.
Security forces in Saxony-Anhalt are also on alert.
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Gunmen reportedly targeted a synagogue and a kebab shop in Halle on Yom Kippur, killing at least two people.
Special forces policemen guard the scene.
Witnesses told German media they saw a man open fire wearing camouflage before fleeing in a auto.
"The grenade hit the door and exploded", he said.
Witnesses told local media outlets that a man fired shots and threw a grenade-like object at a kebab shop. I was not sure that there is one so I silently locked myself up in the toilet, wrote to my family that I love them and waited what might happen.
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Regional broadcaster MDR shared a bystander's cellphone video showing a person wearing a helmet firing shots from a rifle, though it's not clear what the person was shooting at. People in the area were advised to stay in their homes.
"According to what we now know we have to assume that it was at least an anti-Semitic attack", Mr Seehofer said in a statement.
Information about a motive or possible targets was not immediately clear.
The shooting, which took place on the last day of the Jewish holiday of Passover, sent shock waves through the local community.
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