"The Gamaa Islamiya in Egypt stresses the lack of truth in what Aljazeera aired by Dr Ayman al-Zawahiri about it joining al-Qaeda, and categorically denies this," the group said in a statement on its website.
And a former official in Egypt's Gamaa Islamiya said that even if some members had joined al-Qaeda - as al-Qaeda deputy leader Ayman al-Zawahiri said in a video aired on Aljazeera on Saturday - it was unlikely that most would do so.
The group fought a bloody campaign against the government in the 1990s to set up an Islamic state before declaring a truce in 1997.
Sheikh Abdel Akher Hammad, a former Gamaa leader, told Aljazeera on Sunday from Germany: "If [some] brothers ... have joined, then this is their personal view and I don't think that most Gamaa Islamiya members share that same opinion."
No al-Qaeda support
Egypt analysts have downplayed al-Zawahiri's announcement that a "big faction" of the Gamaa had switched over, saying there was no evidence al-Qaeda had major support within the group's ranks.
In the video, al-Zawahiri named Mohamed al-Islambouli as one of those who joined al-Qaeda, referring to the Gamaa leader whose brother Khaled killed Anwar Sadat, the then Egyptian president, in 1981.
A man introduced by al-Zawahiri as another Gamaa leader, Mohamed Hakaima, later appeared in the video to confirm the unity move. But several analysts said he was not a major player.
Diaa Rashwan, a specialist on Islamist groups at the al-Ahram Centre for Political and Strategic Studies, said Hakaima "doesn't represent anybody here in the country", describing him as a "low-ranking member" of the group.
Egypt detained many thousands of Gamaa members or sympathisers in the 1990s when the group was waging a low-level guerrilla war against security forces, mainly in the south.
But hundreds have since come out of detention after renouncing violence. Gamaa leaders declared a truce after a deadly 1997 attack on tourists in Luxor.
Analysts said they did not expect any change in the group's policy after the al-Qaeda announcement, saying its leadership had clearly chosen to avoid violence in Egypt.