The fugitive Islamic State leader, Abu Bakr al-Baghdadi, has appeared in a propaganda video for the first time in five years, in which he recognises the terror group’s defeat in the Syrian town of Baghuz.

The appearance is only Baghdadi’s second on video, and comes weeks after the remnants of Isis were ousted from their last organised stronghold in the eastern Syrian desert. Looking heavier than when he proclaimed the existence of the now collapsed caliphate in mid-2014, Baghdadi blames its demise on the “savagery” of Christians.

Sitting cross-legged alongside a Kalashnikov rifle, he speaks for no more than 40 seconds, and appears to be limited in his movements. “Truthfully, the battle of Islam and its people against the cross and its people is a long battle,” he says. “The battle of Baghuz is over. But it did show the savagery, brutality and ill intentions of the Christians towards the Muslim community.”

The appearance seemed designed to acknowledge the loss of the remaining pockets of Isis territory and to demonstrate that Baghdadi is still alive. He has released several audio sermons in recent years, the last of which was in August last year, but his long absence from public view had fueled speculation that Baghdadi remained impaired from wounds or may have been killed.

Written in text on the video, but not spoken by Baghdadi, is a reference to the Easter bombings in Sri Lanka, which killed more than 250 people in churches and hotels. The attacks’ plotters claimed allegiance to Isis, but it remains unclear whether the group inspired, or directly plotted the carnage.

“Americans and Europeans failed as we congratulate our brothers in Sri Lanka for their allegiance to the caliphate,” the text says. “And we advise them to stick to the cause of God and unity and to be a thorn in the chest of the crusaders. We ask God to accept their martyrdom and help the brothers fulfil the journey they started.”

After the video emerged, the US said it would track down and defeat surviving Isis leaders. The US-led coalition will fight across the world to “ensure an enduring defeat of these terrorists and that any leaders who remain are delivered the justice that they deserve”, a state department spokesman said.

Regional and western intelligence officials believe that Baghdadi’s grip on Isis has slipped since late last year, when a series of defeats at the hands of a Kurdish-led ground force, and a US-led air campaign, forced the group’s senior leader into their last redoubt, a forsaken corner of Syria on the banks of the Euphrates.

Intelligence officials believe a series of rolling battles started last September between Baghdadi loyalists and another faction determined to oust him. Officials say dissent within the ranks culminated in a gunfight on the night of 7 January, which led Baghdadi to flee Baghuz with his bodyguards. He is believed to have since crossed into Iraq, and it is thought he could be hiding in Anbar province in the west of the country.

Officials suggest that a senior Isis figure, Abu Muhammad al-Husseini al-Hashimi, believed to be a distant cousin of Baghdadi, is instrumental in a move against him. Hashimi recently released a 231-page book calling for an uprising against Baghdadi, and for allegiance to be pledged to a new leader.

The book, titled Keep Back the Hands from Allegiance to al-Baghdadi, emerged just as Isis was losing the last of the territory in Syria. It is thought to be the first open challenge to the Isis leader’s authority from within the group’s senior ranks.

In it, Hashimi claims Baghdadi is a ruthless ruler who destroyed the legacy of Isis through oppressive and excessively violent behaviour. He urges any remaining members of Isis to revolt against Baghdadi’s leadership, marking what some have described as the emergence of a reformist or dissident strain within Isis “that believes that extremists gained too much influence” within the organisation.

The criticisms in the book are not universally held among Islamists but there is particular concern about Isis’s treatment of Islamic scholars in recent years, and that attacks on them demonstrate that Baghdadi cannot be considered a true caliph.

As Isis crumbled, the group’s security arm became ever more ruthless in its efforts to crack down on dissent. Islamic scholars and jurists who were perceived to pose a threat to Isis’s claim on theological authority were frequently executed.

The killings led to a schism between middle echelons of the group and some senior officials, who surrendered in Baghuz and have since told their captors of increasing rancour in the caliphate’s dying days.

While no longer able to control territory, Isis is believed to be regrouping in towns and villages on both sides of the Syrian border, and planning for a return to the years of insurgency that followed the US invasion of Iraq.