"With the massive volume of videos on our site, sometimes we make mistakes. When an error is brought to our attention we act quickly to reinstate the videos in question," a YouTube spokesperson told AFP on condition of anonymity.
YouTube sent the Observatory an email on Sunday that said its channels "syrianhro" and "almrsd" had "violated the policy of the site by publishing shocking and offensive videos," the Britain-based watchdog said.
The Observatory, which disseminates graphic videos on YouTube of atrocities from the bloody civil war the UN says has killed more than 60,000 people, condemned the closure.
"This is the second time in two months that the site administration has closed the Syrian Observatory for Human Rights channel," it said in a statement, in reference specifically to almrsd.
It criticised the "lack of awareness by the YouTube administration about the value of what is being published, that global media depend on these videos to know what is transpiring on the ground."
Since the Syrian uprising began in March 2011, the Observatory has published daily reports on nationwide violence and given breakdowns for death tolls.
With its network of Syria-based activists and medics in civilian and military hospitals, it has become a major source for information on events on the ground due to heavy restrictions imposed on foreign media.
The United Nations recently denounced a "proliferation of serious crimes including war crimes" in Syria, as ever more horrifying images and videos emerge from the country.
Both channels have now been reinstated.