The ban, which will continue in Pakistan until further notice, centres on a trailer for a forthcoming film by Dutch politician Geert Wilders.
According to the Pakistan Telecommunication Authority, it portrays Islam as a fascist religion prone to inciting violence against women and homosexuals.
The PTA has also blocked websites showing the controversial Danish cartoons of the Prophet Muhammad, which were reprinted by at least 171 Danish newspapers last week, after originally being printed in 2005.
The authority is urging internet users to write to YouTube and request the removal of the films, saying that the authorities would stop blocking the video-sharing site once they are removed.
The YouTube website was inaccessible in many countries for more than an hour on Sunday. A YouTube spokesperson, said: "For about two hours, traffic to YouTube was routed according to erroneous internet protocols, and many users around the world could not access our site.
"We have determined that the source of these events was a network in Pakistan.
"We are investigating and working with others in the internet community to prevent this from happening again."
The BBC News website's technology editor, Darren Waters, says that to block Pakistan's citizens from accessing YouTube it is believed Pakistan Telecom "hijacked" the web server address of the popular video site.
In protest over the cartoons, hundreds of Islamists in Karachi set fire to effigies of the Danish prime minister and the cartoonist yesterday. There have also been similar protests around the world earlier this month.
Last month, police in Copenhagen uncovered a plot by three Islamic extremists to kill the cartoonist. In response, Danish newspapers republished the cartoon, which showed Muhammed wearing a turban in the shape of a bomb with the fuse lit.
Last week, The Observer and The Wall Street Journal were banned in Egypt after they printed pictures linked to the controversial caricature of the prophet.
Pakistan is not the only country to have blocked access to YouTube. Turkey blocked the site in January in response to video clips insulting the country's founding father, Kemal Ataturk.
It was also banned for four months in Thailand last spring after the government regarded clips as offensive to King Bhumibol Adulyadej.