The internet has become a key propaganda tool for extremist groups
Key websites used by al-Qaeda have been closed for the past six weeks, fuelling speculation they have been targeted by hackers or intelligence agencies.
One site, al-Ekhlas, has long served as a message board for various jihadists but now merely boasts a message by "Your Joker.com Team".
Al-Ekhlas and other such sites have all suffered occasional glitches, but they have rarely been down for so long.
Some jihadists have blamed western intelligence groups for the disruption.
The sites, which also include al-Firdaws, disappeared shortly before 11 September, the seventh anniversary of the attacks on New York and Washington, news agency AFP reported.
Al Fajr Media Center, al-Qaeda's communications wing, put the problem down to technical difficulties.
"We deny reports published by the media of the tyrants regarding the fall of some of the headquarters of these networks into the hands of the enemy," its statement said, according to the US-based Site Intelligence Group, which monitors extremist sites.
The internet has become an increasingly important tool for al-Qaeda, allowing the group to keep in contact with its supporters and spread its message to the outside world.
Some jihadists blame western intelligence agencies, particularly the United States, seeing it as an attempt to stop al-Qaeda getting out propaganda to coincide with the 9/11 anniversary.
Another theory is that the sites have been targeted by Shia Muslim groups engaged in tit-for-tat sectarian cyber warfare with rival Sunnis.
That is a view supported by Mustafa Alani of the Gulf Research Centre in Dubai, who told the BBC that what was once a sectarian war between Sunnis and Shias has "transferred over to a cyberwar".
Analysts say the disappearance of these sites will be a cause of concern for hard-line al-Qaeda supporters.
However many other extremist websites remain operational.