Pakistan Information Minister Sheikh Rashid Ahmad said that all copies of Newsweek's 28 July edition would be confiscated.
“There is a religious article which can provoke Muslims,” he said, adding it would be better for the publishers themselves to withdraw the issues.
The article raising eyebrows concerns the Quran, Islam’s holy text.
When asked whether the magazine was concerned the edition would be banned from other countries, Newsweek Director of Communications Ken Weine said: “We stand behind the article.”
Rashid insisted freedom of speech exists in Pakistan, saying Newsweek had previously written critical articles about the country and the magazine was sold.
Pakistan, a country of 145 million predominantly Muslim people, has laws prohibiting religious incitement.