The radical Islamist cleric Abu Qatada has been cleared by the Jordanian state security court of terrorism offences relating to an alleged 1998 bombing plot.

The international terror suspect, a Jordanian national, was sent back to Amman from Britain last summer after a long legal battle that was only resolved after the home secretary, Theresa May, secured a treaty that guaranteed he would not face a trial that involved the use of evidence obtained by torture. Abu Qatada told the home secretary in May 2013 that he was prepared to return voluntarily to Jordan once the "fair trial" treaty had been put in place.

He was flown back in July last year, 12 years after he was first arrested and detained in Britain in the immediate aftermath of 9/11.

British judges said the cleric was a key figure in al-Qaida-linked activities in Britain, with a wide support network, and remained a threat to national security. They described him as a "truly dangerous individual".

Abu Qatada was convicted in absentia on conspiracy charges in relation to bomb attacks that took place in Jordan in 1998 and 2000. A panel of civilian judges sitting in the state security court in Amman cleared him of the conspiracy charges relating to his alleged role in the 1998 bomb plot.

A verdict on the second set of charges, relating to the "millennium bomb plot" of 2000, was adjourned until September.

The Home Office security minister, James Brokenshire, said: "Abu Qatada's retrial in Jordan has been made possible thanks to this government's determination to successfully deport him from the UK.

"While the courts in Jordan have acquitted Qatada of one of the two charges against him, it is right the due process of law is allowed to take place in his own country. We await a verdict on the remaining charge.

"The UK courts agreed that Qatada posed a threat to national security in the UK, so we are pleased that we were able to remove him. He is subject to a deportation order which means he will be unable to return to the UK."

Downing Street swiftly reinforced the message that he would not be allowed back. The prime minister's spokesman said: "He can't come back, and he won't come back. He is a Jordanian and he does not have a UK passport. He is also the subject of an indefinite deportation order as well. He would not be granted permission to enter the UK, end of story."

Abu Qatada's lawyers told a bail hearing in London in May 2013 that the "fair trial" treaty with Jordan meant that for the first time in 12 years he felt safe returning to Amman.

A British judge referred to the case against Abu Qatada in Jordan as "extremely thin" once the torture-tainted evidence had been discounted.

The Bethlehem-born Qatada, 51, was originally sentenced to life with hard labour in absentia for masterminding al-Qaida-inspired attacks on the Modern American School and a hotel in Amman in 1998. He was subsequently sentenced to a further 25 years in his absence for being involved in a plot to bomb people attending millennium celebrations in Jordan in 2000.

During his retrial, Qatada's defence team attacked the credibility of alleged tape recorded conversations between him and two fellow Salafists who were his co-defendants. One of them was released in 2011 on a general pardon and is believed to be fighting alongside Islamist militias in Syria.