Allegations by the Pakistani government against Qari Saif Allah Akhtar has made him one of Pakistan's most wanted men, which led to his deportation.
"Yes, we confirm that Qari Saifullah Akhtar has been handed over to us by UAE authorities," Pakistan Information Minister Shaikh Rashid said in Islamabad on Sunday.
"He was wanted in terrorism cases" and is being questioned by Pakistani investigators, Rashid added.
Akhtar was wanted in connection with two attempts to kill Musharraf in December last year and was arrested in Dubai last week, Pakistan intelligence sources said.
The suspect is the head of Pakistan's Harkat Jihad-e-Islami group and spent most of his time living in Afghanistan where the Pakistani government alleges he had interacted with the Taliban.
Rashid said Akhtar's arrest was not linked to the July arrests of alleged al-Qaida suspects Ahmad Khalfan Ghailani and computer engineer Naaim Nur Khan.
"He [Akhtar] was more active in Afghanistan and his arrest is yet another major success of Pakistan in the international war against terrorism," Rashid said.
"His arrest is yet another major success of Pakistan in the international war against terrorism"
Pakistan information minister
"His arrest may lead to the arrest of other members of his group," he added.
Intelligence officials have said another leader also linked to the al-Qaida network, Fazl Al-Rahman Khalil, was in Pakistani custody and being interrogated after being arrested two months ago.
The officials said he was closely linked to Taliban leader Mullah Muhammad Umar.
South Africans arrested
Two South African citizens, Zubair Ismail and Fairuz Abu Bakr Ganchi, were also arrested by Pakistani authorities who claimed another "al-Qaida link", and have created a media frenzy regarding possible "attacks in South Africa".
One is a student and the other a medical doctor who frequently volunteered for humanitarian projects. They were arrested with a group of 15 people in Pakistan's Gujarat province a few days ago.
The South African government, however, strongly denied these statements, saying it had credible intelligence that these "possible attacks are untrue".
South African Deputy Foreign Affairs Minister, Aziz Pahad, also said all diplomatic procedures had gone "out of the window" in this case since Pakistani authorities had refused SA diplomats access to the two suspects, citing "security and intelligence reasons".