His former deputy, Maj-Gen Zandisile Ngwanya, testified that Sebe had been "untouchable" in spite of his misuse of power and pilfering from State coffers.
Sebe earlier told the commission he ordered the bombing of a bottle store and a house in an attempt to thwart a South African Military Intelligence operation to overthrow his father's government.
His admission, on the first day of the commission's amnesty committee hearings in East London, was followed by a witness saying he was the most feared man in the former homeland during the time of his father's rule.
Sebe has applied for amnesty for the 1989 bombings on the grounds that they were politically motivated and not the result of a personal vendetta, as two judges ruled in separate trials in 1990.
He is serving a 21-year sentence at Middledrift prison.
The five-member committee, chaired by Judge Hassan Mall, heard that Sebe, as head of the Ciskei Police's Elite Unit, thought nothing of ordering the arrest and detention of people who disagreed with him or who were considered rivals for a woman's affection.
"The applicant was feared by everybody in Ciskei. Nobody could touch him," Ngwanya said.
"He detained a person because of a girlfriend under Section 26 of the Security Act. If he had a quarrel with a person he would call the police and the person was detained in the cells."
The committee was also told that Sebe had been instrumental in the detention for 108 days, and rapid demotion, of a senior civil servant in his father's office who was suspected of being a sympathiser of a banned organistion.
Fikile Gatya, a co-owner in the bombed bottle store, was demoted from his position as secretary-general to that of a principal clerk and transferred to a government office in Whittlesea.
He told the committee he was not questioned by police during detention.
Monday's hearings often became bogged down as Sebe's legal counsel explored the labyrinthine complexities of politics in the former Ciskei and Transkei, as well as the bitter family feud which led to Lennox Sebe's brothers, Namba and Charles,fleeing into exile in Transkei.
In his testimony to the committee, Kwane Sebe admitted to ordering the destruction of the Keiskammahoek bottle store and a Peddie home belonging to Ngwanya, who at that time was serving a two-year prison sentence relating to the death in detention of Eric Mntonga, a former regional director of the Institute for a Democratic Alternative for South Africa.
Sebe testified that the bombings had been aimed at disrupting the work of a secret underground organisation bent on overthrowing his father's government.
The organisation, known as Iliso Lomzi (Eye of the Nation) was a Transkei-based organisation headed by his exiled uncle,Charles Sebe, who was later killed in a bid to overthrow the military government of Brigadier Oupa Gqozo.
Sebe told the committee Iliso Lomzi had been a front for Military Intelligence as part of Operation Katzen.
The operation had been launched by MI with the aim of "setting the whole Eastern Cape ablaze by massive destabilisation of the area, including the overthrow of the then Ciskei Government".
He claimed the bottlestore had been used by MI to channel funds to the organisation, while the house had been built with Iliso Lomzi funds as a safe house.
"The committee must understand that we were working under abnormal circumstances. We were under pressure to respond to the threat and counter it," he said.
However, Ngwanya said the attacks stemmed from comments he had made during his trial on charges of defeating the ends of justice in the Mntonga case.
Ngwanya said he had questioned why Sebe, as head of the Elite Unit, had not also been arrested in connection with Mntonga's mysterious death when so many other members of the unit had been implicated.
Sebe had visited him in prison and ordered him to make a retraction, which he refused to do.
"He said he would destroy my property and would wait for me until I was released from prison".
Sebe allegedly tried to force prison officials to humiliate Ngwanya by making him clean out pigsties.
Sebe's legal counsel, Viwe Nontshe, argued that his client had nothing to fear from Ngwanya's statement in court as Idasa's then national director, Dr Alex Boraine, had already cleared him of any involvement in a letter written to Lennox Sebe.
In the letter, Boraine, now deputy-chairman of the TRC, complained to the Ciskei President about the handling of the inquest into Mntonga's death.
He also named the people thought to have been involved in the murder while clearing Kwane Sebe of any knowledge of the crime.