They were members of Jamaah Ansharut Daulah (JAD), an extremist group responsible for deadly suicide bombings at churches in Indonesia's second-biggest city Surabaya last year, State Intelligence Agency chief Budi Gunawan told reporters in Jakarta.
JAD is among dozens of radical groups that have pledged loyalty to the Islamic State group in Indonesia, which has long struggled with Islamist militancy.
Wiranto, 72 -- who police have said was one of several targets in an earlier failed assassination plot -- was rushed by helicopter to the capital where he was treated for two knife wounds in his stomach.
"He is currently in surgery and I ask that all Indonesians pray that he gets well soon," said President Joko Widodo.
"And I ask for everyone's help in fighting radicalism and terrorism because we can only do it together," he added.
The assassination attempt comes just over a week before Widodo kicks off a second term as leader of the Southeast Asian archipelago of some 260 million people, the world's biggest Muslim majority nation.
Three others -- a local police chief and two aides -- also suffered knife wounds in Thursday's attack but authorities said they had non-life-threatening injuries.
An eyewitness told an AFP reporter that the female attacker was dressed in a body-and-face-covering niqab.
"When the car stopped, there were people circling around, protecting him," he said.
"But a man got into the circle and stabbed Wiranto. The woman also tried to stab him. He was arrested and the woman fought the police."
Last year, JAD staged a wave of suicide bombings by families -- including young children -- at churches in Surabaya, killing a dozen congregants.
Many past attacks by Indonesian militants have been against police and other state symbols.
Authorities routinely arrest suspected IS-loyal militants that they claim were planning bomb and other attacks.
"JAD members are targeting what they call Ansharut Thagut (tyranny) and that includes senior government officials," said Muhammad Syauqillah, program director of the University of Indonesia's Terrorism Study Centre.
Wiranto, the retired chief of the armed forces and a failed presidential candidate, was appointed to his post in 2016 and oversees several departments, including the foreign affairs and defence ministries.
He has faced controversy over alleged human rights violations and allegations of crimes against humanity linked to Indonesia's brutal occupation of East Timor.
In May, police said Wiranto and three other top officials were targeted in a failed assassination plot linked to deadly riots in Jakarta after Widodo's re-election victory.
A group of six people -- arrested before they could carry out the killings -- planned to murder the officials and an election pollster in a bid to plunge the country into chaos, police said at the time.
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