Rukhanah, the mother of Fathur Rahman al-Ghozi, told journalists “whatever amount is promised … if God wishes him not to be captured then he will not be captured".
The Indonesian's escape on Monday from a Philippine police detention centre has sparked an alert across much of Southeast Asia.
Philippine officials admitted one police guard had been asleep and another was out shopping when al-Ghozi and two other inmates strolled out of their cell.
Severely embarrassed by the blunder, the government has offered a reward of just over $93,000 dollars for his recapture.
Jakarta has expressed its concern at the escape, especially as it is still in the process of arresting and convicting the JI perpetrators of the Bali bombings which killed 202 last October.
Rukhanah said she had no contact with her son since his escape.
"Whatever he has done, it would not have been possible unless Allah did not wish it so"
Mother of JI fugitive
Al-Ghozi's mother also declined to comment on Manila's decision to promise a larger sum for her son than the reward for two Filipino members of the Abu Sayyaf who escaped with him.
"That is entirely the business of the government there, it is not for me to comment," she said calmly.
"All I can say is that whatever he has done, it would not have been possible unless Allah did not wish it so," she said, speaking by telephone from her home at Madiun in East Java.
Rukhanah said she and her family would pray for her son's safety but preferred not to see him for his own safety.
Release not until 2020
Al-Ghozi is serving 17 years for possession of explosives and was one of the most senior JI operatives ever to be caught by Asian law enforcement agencies, according to Philippine officials.
He was also a suspect in an August 2000 Jakarta bombing that killed two people and seriously wounded the Philippine ambassador outside his residence.
Indonesian police are on heightened alert at airports and seaports in case al-Ghozi tries to return home.