Hamza appeared for his arraignment before US District Judge Katherine Forrest in Manhattan federal court.
He was among four terror suspects who were flown in from the UK over the weekend to face terrorism charges after having fought extradition to the US for years.
He had made his initial appearance in a federal court here on Saturday and was ordered held in custody till his arraignment.
Two other men, Khalid al Fawwaz and Adel Abdel Bary, have been accused in a conspiracy that resulted in the 1998 attacks on US embassies in Kenya and Tanzania, which killed 224 people.
They have been charged with conspiring with members of al-Qaeda to kill American nationals and to attack US interests abroad. The two have also entered not guilty pleas.
Hamza faces 11 charges, including hostage-taking in Yemen in 1998 that resulted in four deaths, a conspiracy to establish a terrorist training camp in Oregon in 1999 and supporting violent jihad in Afghanistan in 2000 and 2001.
He faces a maximum term of life imprisonment.
New York: Radical Islamic cleric Abu Hamza al-Masri Tuesday pleaded not guilty to charges he plotted to set up a terrorist training camp in the US and provided material support to al Qaeda during his second appearance in a federal court days after being extradited from the UK.
First Published: Tuesday, October 09, 2012, 22:02