The report, titled "We Do Unreasonable Things Here" and based on the accounts of 19 former detainees and the family of another, claimed Egyptian authorities used arbitrary arrests, enforced disappearances and torture.
In a statement released on Wednesday, Egypt's foreign ministry lambasted the report, saying it defamed the country and ignored progress made on human rights in recent years.
"The report ... is a new episode in a series of deliberate defamation by such organization, whose politicized agenda and biases are well known and reflect the interests of the entities and countries sponsoring it," said foreign ministry spokesman Ahmed Abu Zeid.
In the report, the New York-based rights group said security services in Egypt used torture as a "systematic practice" against suspected opponents of the government.
"Egyptian authorities keep insisting that any incidents of torture are isolated crimes by bad officers acting alone, but the Human Rights Watch report proves otherwise," Joe Stork, deputy Middle East director at Human Rights Watch, said on Thursday.
"Rather than address the torture crisis in Egypt, the authorities have blocked access to a report that documents what many Egyptians and others living there already know."
According to the report, the statements of the detainees interviewed reflected how "police and officers of the National Security Agency regularly use torture during their investigations to force perceived dissidents to confess or divulge information, or to punish them".
One position, called the "chicken" or "grill", "involved laying suspects on their back, placing their knees over a stick or bar, wrapping their arms around the bar from the other side so that the bar lays between the crook of their elbows and the back of their knees, and tying their hands together above their shins to secure the position".
The bar was then lifted, placing the suspects in a position "resembling a chicken on a rotisserie spit".
In most cases, officers stopped using torture once they obtained confessions or the names of suspects' friends and acquaintances, according to the HRW report.
Egypt first blocked access to a number of news websites including Al Jazeera and Huffington Post Arabic in May after similar actions by its Gulf allies Saudi Arabia and the United Arab Emirates.
Since then, hundreds of other news sites and blogs have been wiped from Egyptian screens with the most recent count at 424, according to the Association for Freedom of Thought and Expression, a non-governmental organisation tracking the affected sites through software that monitors outages.
The government has offered no comment on the reason behind the blockages.
Source: News agencies