Paris-based Reporters Without Borders (known by its French acronym, RSF) said in a statement on Tuesday: "These journalists have been denied justice and not allowed to see family or lawyers."
Al-Hajj is being held at a military base in Guantanamo Bay in Cuba, and Abdel Amir Yunes Hussein, 26, who works for US network CBS News, is being held at a US prison in Iraq.
The statement accompanied a new report into the arrests of journalists in Iraq and Afghanistan.
RSF also said it was investigating the detention by US authorities of three journalists working for Reuters in Iraq although they were recently released.
The US government made no immediate comment on the report.
Al-Hajj, 36, has been held at Guantanamo Bay since 2002 after being arrested in Afghanistan in 2001, it said.
He has been accused of making videos of Osama bin Laden.
RSF said he had told a human rights lawyer who visited him in Guantanamo that he had been interrogated more than 130 times and tortured, including sexually.
Hussein has been held at the Camp Bucca prison in Iraq since April, the media watchdog said.
It said US authorities suspected him of having ties with insurgents.
Freedom of information
RSF said it was seeking details about the two journalists from the US Department of Defence under the Freedom of Information Act.
Citing the same act, it is also demanding information about the three Reuters reporters.
Majid Hameed, who was working as a freelance reporter for Reuters, was detained in September at a friend's funeral, and Samer Mohammed Noor and Ali al-Mashadani were detained two months apart in 2005. All were released in January.