The cartoons, published in Danish newspapers in 2005 and again earlier this month, angered Muslims because of their depiction of the Prophet Mohammad.
"They asked us to ban it immediately...and the order says the ban will continue until further notice," said Wahaj-us-Siraj, convener of the Association of Pakistan Internet Service Providers.
Publication of the cartoons led to protests and rioting in many Muslim countries, including Pakistan, in which at least 50 people were killed and three Danish embassies attacked.
Several Danish newspapers reprinted one of the cartoons earlier this month after police in Copenhagen uncovered a plot by two Tunisians and a Dane of Moroccan origin to kill the cartoonist, sparking further protests around the world.
Attempts to access YouTube in Islamabad on Sunday were met with a generic error message saying the site was unavailable.
"Users are quite upset. They're screaming at ISPs which can't do anything," Siraj said.
"The government has valid reason for that, but they have to find a better way of doing it. If we continue blocking popular Web sites, people will stop using the Internet."