Muhammad Iqbal Abd al-Rahman, who had been in Malaysian custody for 30 months on suspicion of "terrorist links", never showed up for the flight despite immigration officials telling his family to prepare to join him at the airport.
Abd al-Rahman's wife, Fatima Zahra Abd al-Aziz, said she had learned that his deportation was delayed after she checked in to board the Sunday morning flight from Kuala Lumpur to Jakarta.
"I feel very sad and disappointed. They told me I should come here to the airport," she said. "I had expected to be with my husband today."
Immigration officials refused to comment.
Abd al-Rahman, 46, an Indonesian with permanent resident status in Malaysia, was arrested in June 2001 under the Internal Security Act allowing indefinite detention without trial.
He was released in August but immigration officers revoked his permanent resident status and immediately arrested him pending deportation to Indonesia.
"I feel very sad and disappointed. They told me I should come here to the airport. I had expected to be with my husband today."
Abd al-Rahman's wife
Al-Rahman has appealed to the High Court against a declaration that he is an undesirable person and a prohibited immigrant.
Fatima said her husband was not a wanted man, nor has he any criminal record in Indonesia. They have lived in Malaysia for 20 years and he is just a "simple religious preacher," she said.
No new date has been set for the deportation.
Indonesia has said it would question Abd al-Rahman about his possible links to terrorism if he were sent back to Indonesia.
Abd al-Rahman is suspected of being among the top echelons of the Jemaah Islamiyah (JI), along with Indonesian cleric Abu Bakr Bashir and alleged operations chief Hanbali who is now in US custody.
More than 80 suspected Islamists are currently held
under Malaysia's ISA, a number of them alleged to be JI members.
Officials allege Abd al-Rahman was a close associate of JI's alleged spiritual leader Abu Bakr Bashir, and of Riduan Isam al-Din, better known as Hanbali.
The latter is accused of masterminding last year's nightclub bombings on Indonesia's Bali island that killed 202 people, and other deadly attacks blamed on Jemaah Islamiyah, which is said to have links to al-Qaida.
In January, the US State Department designated Abd al-Rahman a terrorist and called him Jemaah Islamiyah's "primary recruiter and second in command".
Indonesian officials have repeatedly said Abd al-Rahman is not wanted for any crime there, and they have no reason to arrest him.
His case has raised concerns about dozens of other Jemaah Islamiyah suspects detained in Malaysia under the same law.