Qatar's Supreme Council of Information and Technology (ictQatar) said in a statement carried by local media that it has "recovered all government websites hacked on Saturday."
It said it is ready to "deal with any similar future operations."
Signup to our newsletter and follow us on Facebook and Twitter!
"No financial losses have been caused" by the hacking that targeted websites with the "gov.qa" domain name, local media quoted ictQatar as saying on Twitter.
The Qatari interior ministry's page was among the websites hit. But the ministry said on Twitter that "data registered on the website was not affected."
Hackers who claim to support Assad, collectively known as the Syrian Electronic Army, have targeted high-profile websites in recent months, including one belonging to the US marines and the New York Times's page.
Qatar, alongside Saudi Arabia, has openly supported rebels battling Assad's regime since an uprising against his rule broke out in March 2011.