In a new report from the group entitled "Cuba's Repressive Machinery: Human Rights 40 Years After the Revolution", the organisation describes the Cuban Government as the worst abuser of human rights in the region.
But the report is also highly critical of the long-standing US embargo against Cuba.
After 40 years in power, President Fidel Castro" maintains control through intimidation, repressive laws, and by imprisoning dissidents", Human Rights Watch says.
Fidel Castro's security services systematically harass and persecute suspected and real opponents to his government, some of whom are tortured in prison, the report claims.
Independent journalists, religious and human rights activists, doctors and economists are denied basic rights of defence. They are punished for crimes such as "dangerousness", says the report.
'Basic rights denied'
"Cuba stands alone in the hemisphere for this kind of human rights abuse: criminalising free speech and association, imprisoning dissidents, and denying access to international human rights monitors," said Jose Miguel Vivanco, executive director of the group's Americas division.
Cuba, according to Human Rights Watch, lacks such hallmarks of a democratic state as an independent judicial system and access to lawyers. The right to a fair trial is often compromised, it claims.
The group says that religious freedom has grown in recent years, but public expression of faith and humanitarian work by church groups are still restricted.
Human Rights Watch was not able to investigate in Cuba. Instead, it had to compile its report from sources such as telephone interviews and reports by travellers, independent and foreign journalists
Criticism of Washington
But Human Rights Watch is also outspoken in its criticism of the US Government and its trade embargo against Cuba.
"The embargo has become counterproductive to the promotion of human rights," Executive Director Vivanco said.
The BBC Havana Correspondent, Tom Gibb, says, the Cuban attitude is that its treatment of prisoners is an entirely internal affair.
Fidel Castro's government justifies locking up its opponents by branding them as puppets of US hostility against the island.
In the end, the correspondent says, such policies allow Fidel Castro to maintain his grip on power and that appears more important to him than any amount of foreign criticism.
Human Rights Watch wants the European Union and Canada to "take a more active role in promoting human rights."
Although the EU has tied its help for the island to an improvement in its human rights record, Human Rights Watch wants more pressure on Havana.