Israeli police said in a statement that "several law-breaking youths and masked agitators" fortified the mosque "in order to disrupt public order and desecrate the mosque".
"After many and prolonged attempts to get them out by talking to no avail, police forces were forced to enter the compound in order to get them out with the intentions to allow the Fajr [dawn] prayer and to prevent a violent disturbance," it added.
"When the police entered, stones were thrown at them and fireworks were fired from inside the mosque by a large group of agitators."
One officer was injured in the leg by a stone during the clashes, it said.