"Our initial impression was that the guy was Adam Gadahn but that information now looks incorrect," said one security official, who declined to be identified.
The arrested man was believed to be an American who goes by the alias Abu Yahya, the officials said. Gadahn is known to have used a similar alias.
"Probably the name and his origin caused the confusion," the first official said.
He declined to speculate about the identity of the arrested man except to say he was apparently an American al-Qaeda operative.
He said: "We don't know yet how big a catch he is!"
Omar Waraich, a journalist with the Islamabad-based Independent newspaper, told Al Jazeera the arrest showed that Karachi continued to be a popular hideout for Taliban and al-Qaeda operatives.
"It is also a breakthrough for the Pakistanis and Americans that just weeks after the arrest of Mullah Brader [a top Afghan Taliban commander captured recently] and other shadow governors throughout Pakistan, you've got another al-Qaeda operative," he said.
Gadahn has been involved with al-Qaeda's al-Sahab media wing and has appeared in al-Qaeda videos wearing robes and a turban, warning the United States that it would face attacks if it did not heed al-Qaeda demands.
On Sunday, a video was released on Islamist websites in which Gadahn called for Muslims in the United States to launch attacks to undermine the economy, according to a website that monitors al-Qaeda announcements.
The Federal Bureau of Investigation has been seeking to question Gadahn since May 2004, and the US government has offered up to $1m in reward money for information leading to his arrest.
The 2006 treason charge against him carries a maximum penalty of death.