Deputy Prime Minister Abdullah Ahmad Badawi said on Monday that Hambali's Malaysian wife, Noralwizah Lee Abdullah, is being held under the Internal Security Act (ISA).
"We think Hambali's wife has useful information for us. She is certainly important as far as we are concerned," Badawi said.
Police chief Norian Mai said her interrogation had already began.
Hambali, an Indonesian, married Noralwizah when he lived in Malaysia where he had permanent residence status.
He is the alleged operational chief of the Jamaa Islamiya network blamed for the Bali bombings.
"We think Hambali's wife has useful information for us. She is certainly important as far as we are concerned"
Abdullah Ahmad Badawi
Deputy Prime Minister
Hambali is said to be in the custody of the United States after his capture in Thailand last week, but his whereabouts have not been revealed.
Dozens of alleged members of Hambali's JI network are already jailed in Malaysia under the ISA.
Badawi said the focus now was to capture two Malaysian JI members, Azahari Husin and Noordin Muhammad Top, who are believed to be bomb makers.
Azahari is alleged to be the organisation's top explosives expert, and is suspected of involvement in the Bali bombings and the attack on the Marriott Hotel in Jakarta.
"We are looking for them. Indonesia is also looking for them. They can be anywhere. In Southeast Asia or outside the region," Badawi said.