A police statement says the red and black Nazi symbols were discovered by a guard at the monument and were immediately wiped off the seven slabs affected.
The swastikas, in red and black, measured between 20 and 60cms, police said. The memorial covers 19,000 square meters in the heart of the capital and is a labyrinth of charcoal grey concrete plinths.
The memorial to the Holocaust's 6 million Jewish victims is a field of gray slabs situated close to Berlin's Brandenburg Gate.
The vandalism discovered on Saturday came a week after a memorial to gay victims of the Nazis was also damaged.
The Associated Press and Reuters contributed to this report