Pakistani forces helped in the raids on suspects
US Defence Secretary Donald Rumsfeld said that was "a very senior al-Qaeda official",
He confirmed that the suspect had been shot while trying to escape last week, but said his wounds were not life-threatening.
White House spokesman Ari Fleischer told journalists that Abu Zubaydah was a "key terrorist recruiter and operational planner and member of Osama bin Laden's inner circle".
If confirmed, he would be the highest ranking member of al-Qaeda to fall into American hands since 11 September.
The spokesman said that the location where the suspect was being held would be disclosed, for security reasons.
"He will be interrogated about his knowledge of ongoing plans to conduct terrorist activities." said Mr Fleischer.
Abu Zubaydah was apprehended in an overnight raid on Wednesday when about 60 people, including 29 mostly Arab and Afghans, were arrested by Pakistani and US security forces.
They are now in US custody.
Senior commander
Abu Zubaydah - also known as Zayn al-Abidin Muhammad Husain and Abd Al-Hadi Al-Wahab - serves as Bin Laden's senior field commander.
He is believed to have been born of Palestinian parents in Saudi Arabia, and has strong connections with Jordan and Palestinian groups.
Abu Zubaydah has been sentenced to death in Jordan, and is believed to have links to many of al-Qaeda's anti-US operations.
When Bin Laden and his inner circle called for an attack, it was Abu Zubaydah who would contact the cells in the field to conduct them, the US authorities say.
US officials allege that he organised several attacks on US interests, including the millennium plots to blow up Los Angeles International Airport and a hotel in Jordan frequented by American tourists.
Abu Zubaydah is also alleged to have worked in Pakistan recruiting and vetting al-Qaeda volunteers, arranging their training and assigning them to terrorist cells.
US officials say he knows the names, faces and locations of al-Qaeda operatives the world over and may even know the whereabouts of Osama Bin Laden if he is still alive.