The Pakistan Telecommunication Authority told Internet service providers to restore access to the site after the removal of what it called a "blasphemous" video clip, authority spokeswoman Nabiha Mahmood said.
Pakistan ordered the site blocked on Friday over a clip featuring a Dutch lawmaker who has said he planned to release a movie portraying Islam as fascist and prone to inciting violence against women and homosexuals.
A Pakistani official told CBS News reporter Farhan Bokhari that an investigation was being conducted to determine why Pakistan's action resulted in the blocking of YouTube in other nations.
"Frankly we are all a bit puzzled because nobody imagined that such an action in Pakistan could lead to the kind of reaction we saw," the official said.
Mahmood said the Pakistani authority had posted a complaint through the Web site - a facility open to any registered user - but had not been in contact with the administrators of YouTube.com, which is owned by Internet giant Google, Inc.
While several other videos featuring the politician, Geert Wilders, would remain visible to Pakistani Internet users, Mahmood said the one which was removed had been "totally anti-Quranic" and "very blasphemous."
She said it promoted Wilders' upcoming movie, but provided no details about its content.
The authority aimed to restrict the site only in Pakistan, but the move inadvertently cut access for many of the world's Internet users for up to two hours on Sunday.
YouTube said the next day that it was caused by a network in Pakistan.
"We are investigating and working with others in the Internet community to prevent this from happening again," YouTube said in an e-mailed statement.
Mahmood said the Pakistani regulator carried no responsibility for "technical hitches" which may have lead to problems elsewhere. She said it was not clear how that occurred.
Pakistani officials hope to prevent a repeat of violent anti-Western protests that erupted in early 2006 after a Danish newspaper published cartoons of the Prophet Muhammad regarded by many Muslims as offensive.
Danish editors reignited the controversy earlier this month by reprinting a cartoon that shows the prophet wearing a bomb-shaped turban.
On Tuesday, about 300 students rallied at a university in the Pakistani city of Multan carrying banners denouncing Denmark, the United States and Pakistani President Pervez Musharraf. It was the latest in a series of small protests by Islamic students in the country.
Umer Abbasi, a leader of the protest, urged all Muslim countries to follow Pakistan in blocking offensive material on the Internet.
"If you look deeply, America can be seen behind all anti-Muslim moves around the world," Abbasi told the crowd, who later burned Danish and American flags.
Abdullah Riar, Pakistan's minister for information technology and telecommunications, said authorities wanted to prevent Islamic hard-liners from seizing on the Wilders clips.
"We are already in the spotlight on the issue of intolerance and extremism and terrorism and this is something that somebody is doing by design to excite and insinuate Islamic sentiments," Riar said.
He said the indirect effects were "very sad, very unfortunate. We have nothing against the YouTube site itself."