"He said lawyers were not present during any of the interrogation sessions, where, he alleged, prosecution officials had intimidated and threatened him and other witnesses," the New York-based rights group reported.
Kadhafi's third oldest son spoke to HRW without guards present on September 15 at Al-Hadba prison, in what appeared to be his first meeting with a rights organisation since his extradition from Niger in March 2014, it said.
Saadi Kadhafi had sought refuge in Niger after the 2011 popular uprising that toppled his father.
He is charged with the first-degree murder in 2005 of a former trainer at Tripoli's Al-Ittihad football club and his trial is underway.
Saadi Kadhafi, 42, told HRW researchers that he had no legal representation during the pretrial and investigation phase of his case, although he was able to appoint a lawyer around the start of his trial.
He said he had been "held in solitary confinement at Al-Hadba prison since his extradition in a windowless cell, though with a fan, and has had no communication with other detainees," HRW said.
Researchers met with three other detainees including former military intelligence chief Abdullah Senussi, and two former prime ministers, Abuzeid Dorda and Al-Baghdadi Al-Mahmudi.
A Tripoli court sentenced all three to death in July for their alleged role in suppressing the 2011 uprising.
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Senussi has also been named by British media as one of two new suspects Scottish prosecutors are reported to have identified in the bombing of a Pan Am jet over the Scottish town of Lockerbie in 1988 which killed 270 people.
The three former officials reported lacking private access to lawyers, court authorities refusing to allow them to speak during trial proceedings and armed groups intimidating their lawyers, HRW said.
"One also alleged ill-treatment during interrogations," it added.
In early August, Arabic news website clearnews published a video appearing to show officials and guards at Al-Hadba prison ill-treating several detainees including Saadi Kadhafi.
Libya plunged into chaos after the 2011 uprising and now has two governments and two parliaments vying for power in the oil-rich country.
Al-Hadba is controlled by the Libya Dawn militia coalition, which supports the self-declared authority in Tripoli, rival to the internationally recognised Libyan government in Al-Bayda and Tobruk to the east.
In July, a court sentenced to death another Kadhafi son, his one-time heir apparent Seif al-Islam, for crimes during the uprising.
Seif al-Islam, who is also wanted by the International Criminal Court (ICC), was tried in his absence because he is being held by a militia that opposes the Tripoli authorities.
Three of Kadhafi's seven sons were killed in the uprising. Kadhafi himself was captured and killed by rebels in October 2011.