"Stones were thrown at tourists and police officers, we have made three arrests ... they are the suspects involved in throwing stones," police spokesman Micky Rosenfeld told Agence France Presse(AFP). "The situation is calm at present," he said.
He also said he did not know the cause of the incident.
"It's not clear, it's something that's being looked into," he said, adding that nobody was injured.
A Palestinian protest was staged a week ago at the site, which is revered by Jews as the site of their biblical Jewish temple, when a group of Jewish nationalist hardliners attempted to visit.
They were prevented by police and peace was restored.
The Al-Aqsa compound, known to Jews as Temple Mount, is home to the third-most sacred site in Islam and is venerated by Jews as the site where King Herod's temple once stood before it was destroyed by the Romans in 70 AD.