The New York-based group on Wednesday called on the Tunisian government to "immediately put an end to prolonged solitary confinement" of political prisoners in a 40-page report released in Tunis.
Many of those jailed are activists connected to the banned Islamist Ennahda party, the report said.
Non-governmental organisations say that more than 40 members of the outlawed group have been in solitary confinement for over a decade.
Authorities consider them common criminals with no special status and do not call them prisoners of conscience.
"The Tunisian practice of prolonged solitary confinement not only violates international norms on the treatment of prisoners but it also violates Tunisian law, which authorises solitary confinement for a maximum of 10 days," the report said.
Eric Goldstein, who heads the North African division of Human Rights Watch, said he was encouraged by pledges from Tunisian officials to end the practice of solitary confinement and to allow rights workers to visit Tunisian prisons.
He called the pledges "positive signs" that he hoped materialised in view of putting an end to the "deplorable conditions" in Tunisian prisons.
The North African nation, a US ally in the fight against terrorism, has long been criticised by rights groups for its closed-door political system that bars dissenters, its tightly controlled press and for trampling on civil liberties.