The State Department said Havana's decision to block Internet transmission of the new 14ymedio online newspaper restricted Cubans' "freedom of expression and of the press."
The online daily news website, www.14ymedia.com, was launched Wednesday by renowned dissident blogger Yoani Sanchez.
"The Cuban government continues to limit fundamental freedoms, including freedom of expression and of the press, freedom of assembly, and the free flow of information to, from, and within the island," the US statement said.
"Cubans deserve the right to freely express themselves and the right to petition their government."
The statement added that President Barack Obama "will continue to stand up for those rights and encourage others to do so as well."
Sanchez had hoped that her online media venture would be Cuba's first independent news outlet in 50 years.
People in Cuba who tried to access the site however, were redirected to another page, Yoani$landia.com, filled with attacks on the prize-winning writer and pieces by pro-government bloggers.
People outside Cuba trying to view the site were able to do so without difficulty, however.
The Inter American Press Association on Wednesday issued a statement condemning Havana's "censorship" of the website.
"While this action is no surprise, the world was hoping for greater tolerance by the Raul Castro government, considering its efforts to show a more positive face, more open to raise attention of the international community," said Claudio Paolillo, chairman of the Miami-based group's Committee on Freedom of the Press and Information.
"Unfortunately, this censorship shows that the Cuban government continues to think that freedom of expression is a concession that is granted by the authorities, not a human right, that no one may criticize them and they do not have to give any explanation to their citizens."