"Muslims who have experience in jihad and received an education in it feel obliged to practise it wherever they are," he told the Associated Press.
"They will look for religious justification to carry out [the attacks]."
But while he would not condemn those behind the attacks, he said they were counterproductive as they were rejected by local Muslims.
"We cannot call what they did an act of evil, let alone terrorism.
"But we must see the objective facts: those actions did not bring positive results in efforts to spread the faith in Indonesia. We need to tell them to think again."
Jemaah Islamiyah is the South-East Asian group that the authorities have linked to al-Qaeda and blamed for several attacks in the region, including the 2002 Bali bombings in which 202 people were killed - mostly foreigners.
"We cannot call what they did an act of evil, let alone terrorism. But we must see the objective facts: those actions did not bring positive results in efforts to spread the faith in Indonesia. We need to tell them to think again"
alleged one-time JI leader
Sidney Jones, an analyst with International Crisis Group in Jakarta, said Abu Rusdan's point about groups being influenced by online material "should be taken seriously".
"Many groups are downloading material, including how to set up a terror cell, and translating them from Arabic and Bahasa Indonesia," she told Al Jazeera.
According to Jones, Abu Rusdan became the caretaker leader of Jemaah Islamiyah in early 2002 after the arrests of alleged spiritual leader Abu Bakar Bashir.
She said Abu Rusdan has inside knowledge about radical Islam and knows about the internet's influence on small groups.
"He used to run a computer store in Kudus in central Java, so he would be well aware of the material available on the internet," she said.
"If he is saying these things, then he should be taken seriously."
However, she said that despite Abu Rusdan's warning about more imminent attacks, she thought the situation in Indonesia was "much better than now that it was two years ago".
She said there were groups which have emerged and died away, and new groups were coming up with very radical agenda.
But she added: "Just because the situation has improved doesn’t mean the problem is going away anytime soon."