The military figure in charge of Jakarta's security at the time was last week sworn in as the new defence minister of the world's fourth-most populous nation.
Sjafrie Sjamsoeddin, 72, has been accused by rights groups of abuses during the riots, as well as against separatists in East Timor, Aceh and Papua.
"Human rights enforcement is increasingly bleak," said Maria Catarina Sumarsih, whose son was shot dead in late 1998 by the army after the fall of Suharto.
"We might see Indonesia returning to a militaristic state, like during Suharto's era."
Sjafrie is a close friend of newly inaugurated President Prabowo Subianto, having met at a military academy where they were classmates.
Both made the rank of general, but both have also been implicated in the disappearance of student activists from 1997 to 1998.
According to the Commission for the Disappeared and Victims of Violence, or Kontras, 23 activists were kidnapped between 1997 and 1998.
Nine were found alive -- several who now support Prabowo -- while one was found dead and 13 are still missing.
Prabowo was discharged from the military over the abductions but denied the allegations and was never charged.
Sjafrie was also cleared of any wrongdoing by Indonesian authorities for his role in the Jakarta unrest.
He claimed that police -- who were in joint command with the military -- lost control, according to a Wikileaks cable from the US embassy in Jakarta.
The allegations have had little impact on their popularity, with Prabowo coasting to a first-round election victory with more than 96 million votes.
An independent Indikator Politik poll last week showed 85 percent of Indonesians were confident Prabowo's team including Sjafrie will lead Indonesia to a better future.
"[Sjafrie] is a top red beret person. He was also Suharto's confidant," an X user wrote in Indonesian under a post about his nomination.
"This person's nationalism should not be doubted."
- 'Culture of impunity' -
But executive director of Amnesty Indonesia Usman Hamid said Sjafrie's appointment could hurt "ongoing efforts to address and investigate past abuses".
Sjafrie played a role in the invasion of East Timor in 1975, then later joined the elite army force known as Kopassus.
The unit was used to tamp down internal unrest and to quash a rebellion in the tiny former Portuguese colony.
In a 2009 US diplomatic cable, Sjafrie was implicated in the 1991 Santa Cruz massacre that saw more than 250 unarmed pro-independence protesters shot dead, as well as unrest after a UN-backed referendum in 1999.
"He was present for the Santa Cruz massacre. His claim he was rescuing Western journalists... cannot be confirmed," the US embassy in Dili cable published by Wikileaks read.
"The facts... lead us to conclude that Sjafrie held senior positions of command responsibility in both 1991 and 1999, moments when atrocities undeniably occurred, and strongly indicate his personal culpability."
In later domestic court cases relating to the East Timor unrest, Sjafrie's name was never brought up and he was never charged.
But the US denied him a visa in 2009 when he was an adviser to then-president Susilo Bambang Yudhoyono.
The defence ministry did not respond to an AFP request for comment.
"The lack of will of the state... resulted in Sjafrie being unable to be dragged to the human rights court," said Dimas Bagus Arya, coordinator of Kontras, a committee for those who disappeared.
"The culture of impunity was the cause, and the election of Prabowo... further strengthened the fact that there would be no legal accountability process for military actors."
Sjafrie has proceeded to celebrate Prabowo's rise on Instagram, posting old images of his boss and Suharto.
Harking back to a bygone era, the new defence chief posted a 1989 picture from East Timor showing him standing next to a young Prabowo in military fatigues.
"An old photo that carries meaning," he wrote.
"About the ups and downs in the waves of devotion."
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