He was one of the founding members of a Pakistani militant organisation called Ummah Tameer-e-Nau. He was accused of travelling through Afghanistan without notifying the Government of Pakistan. Along with fellow nuclear scientist Sultan Bashiruddin Mahmood, he was arrested in October 2001 in Islamabad by a joint-operation of the Inter-Services Intelligence and the Federal Investigation Agency, because of their connections to the Taliban.
In the hope of securing a quick release from the intelligence agencies and returning to his research at the PAEC, he readily confessed. The FIA and ISIs joint-Intelligence report, which was given to the Parliaments Committee on National Security and Defence Affairs, stated that Majeed admitted that Osama bin Laden had asked them to build either a radiological or a biological weapon. He was subsequently designated by the Al-Qaida and Taliban Sanctions Committee of the Security Council in December 2001.
American CIA intelligence officials  said that the first interrogation of the two Pakistani scientists concluded that Mahmood and Majeed did not know enough to help build a nuclear weapon. "These two guys were nuclear scientists who didnt know how to build one themselves," the American official said. "If you had to have guys go bad, these are the guys youd want. They didn't know much."