The international organisation's report has questioned South Africa's commitment to constitutional rights and equality.
In its 2013 World Report, the New York-based lobby group also raises concerns about the levels of police brutality and the government's perceived failure to fulfill basic and economic social rights.
Cameron Jacobs, South Africa Director at Human Rights Watch, told the Mail & Guardian that "2012 signified a watershed and wake-up call for South Africa because of events that led to "serious challenges to human rights and the constitution".
He said the Marikana tragedy, the farmworkers' strikes in De Doorns and other violent service delivery protests had put the South African Police Service (SAPS) under the spotlight and there were concerns about the use of "excessive force".
"We are waiting on the final report from Farlam commission of inquiry into what happened at Marikana, to see if it finds the force used was justified in the circumstances," he said. "If it was not found to be justified, then it is important that the rule of law takes effect."
But Jacobs said police behaviour was only part of the story.
"We are increasingly seeing SAPS facing very precarious situations," he explained.
"There needs to be sufficient training for officers to handle these situations, but equally, we need highlight the economic and social rights that are enshrined in the constitution that these people are fighting for," he added.
Regarding the Protection of State Information Bill and the Traditional Courts Bill, Jacobs said Human Rights Watch was monitoring carefully to see how the Information Bill would be applied and what form the Traditional Courts Bill would take after called-for revisions.
He explained: "With the Courts Bill, our major concern is about equality, not just for women but also the LGBT [the lesbian, gay, bisexual and transgender] community. If traditional leaders are allowed to do certain traditional things, then it risks carte blanche violations of our constitution."
And he added: "Freedom of expression and the right to equality are things that we struggled for under apartheid and it seems that these struggles are re-emerging in a democratic South Africa."
In its chapter on South Africa, Human Rights Watch acknowledges the country's leadership in promoting the International Criminal Court though notes it has yet to block African Union decisions which calls for states not to co-operate over the arrest of Sudanese President Omar al-Bashir.
The report also questions the decision to close three of seven Refugee Reception Officers – which "caused a crisis for asylum seekers" – and it says South Africa's tenure as a non-permanent member of the UN Security Council had been marked by "erratic stances on human rights concerns" regarding UN engagement on Libya and Syria.
You can read the full report on 90 countries including South Africa at www.hrw.org.
See the Africa section of the M&G newspaper on Friday.