At least 22 Jordanian police have been taken to hospital after clashes.
Jordanian authorities denied reports that a Syrian refugee had been killed in the unrest.
Security forces used tear gas to disperse stone-throwing refugees who had set fire to tents and vehicles.
The sprawling camp, which houses some 106,000 refugees, has seen several protests since opening two years ago, mainly over poor living conditions.
Zaatari is located in the Jordanian desert, about 7.5 miles from the Syrian border.
It is the world’s second-largest refugee camp – behind Dadaab in eastern Kenya – and has become the fourth largest city in Jordan.
Jordanian authorities said the violence broke out after police arrested a group of refugees trying to leave the camp illegally.
“The rioters burned six tents and two caravans and tried to attack police stations,” the Public Security Directorate said in a statement.
Residents of Zaatari, however, claimed the clashes occurred because a Jordanian policeman had run over a Syrian child.
Eyewitnesses also said the number of refugees injured in the unrest was much higher than the three cases confirmed by officials.
Opened in July 2012 with some 100 refugee families, Zaatari is now made up of roughly 30,000 shelters and administration buildings.
It costs about $500,000 a day to run, with half a million pieces of bread and 4.2 million litres of water distributed daily.
Correspondents say life inside the camp can be harsh, as residents – mostly hailing from the Daraa governorate of Syria, face a number of challenges – the biggest being security.
A second overflow camp – Azraq – is under construction in the desert to meet demand. It too will have the capacity to host up to 130,000 people.
More than 2.5 million people have fled Syria since the civil war broke out there in March 2011.
Earlier this week, the UN confirmed that the number of Syrian refugees registered in Lebanon had surpassed one million, making it the highest per capita concentration of refugees worldwide.
This is followed by Jordan, which houses almost 600,000 refugees, Turkey, Iraq and Egypt.
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