The "As Long As You Love Me" hitmaker wrote in the guestbook that he hoped Frank "would have been a Belieber" if history were different. "Belieber" is what Bieber fans call themselves.
The 19-year-old's note read: "Truly inspiring to be able to come here. Anne was a great girl. Hopefully she would have been a Belieber."
The museum ignited a swarm of controversy after they quoted the singer's comment on their Facebook and Twitter page. Many people commented on the museum's posts criticizing the Canadian star for his insensitivity.
"Way to turn an inspiring moment into something about yourself," read one comment."
"Glad he went, but, the last sentence is VERY self serving. He missed the lessons of Anne totally," read another.
Anne Frank House spokeswoman Maatje Mostart defended the star and said the museum didn't find his remarks offensive.
Anne Frank was a Jewish schoolgirl who hid with her family from the Nazis in the Netherlands during World War II. Her diary, which she wrote during hiding, was recovered and published after the war. She has since become a symbol of the suffering of Jews during the Nazi occupation.
The Associated Press contributed to this report.