Rebels in Libya's western Nafusa Mountains have burned and damaged homes, looted hospitals and shops and beaten suspected regime loyalists during fighting over the past month, according to a report from Human Rights Watch (HRW) released on Wednesday.

The rebel military commander in the Nafusa, Colonel El-Moktar Firnana, admitted to HRW that his forces were responsible for the abuses but said the lootings and beatings had gone against orders and that some rebels had been punished as a result.

But he also sought to explain the attacks, saying they were a consequence of local residents' loyalty to the embattled regime of Muammar Gaddafi.

"People who stayed in the towns were working with the army," he told HRW. "Houses that were robbed and broken into were ones that the army had used, including for ammunition storage ... Those people who were beaten were working for Gaddafi's brigades."

On Wednesday, Mahmoud Jibril, the chief of staff for the National Transitional Council, contradicted Colonel Firnana's admission and flatly denied that any abuses had taken place.

A "few incidents" had occurred during the first two weeks of the uprising, he said during a visit to Brussels, but "this is no longer the case in the liberated areas".

One resident in the town of Rayayinah, however, told HRW that he saw three injured people who claimed to have been beaten by rebels after they swept through, and that others had been hurt as well. One of the injured men had lost two toes when rebels shot him in the foot, the witness said.

The HRW release coincided with recent disclosures about rebel abuses made by New York Times reporter CJ Chivers, who has been writing from the Nafusa.  

On Sunday, Chivers described the recent rebel victory in al-Qawalish, a town some 50km by road from the key Gaddafi-held town of Gharyan, and how the battle had been quickly followed by the looting and burning of homes and shops.

The mayhem underscored the lack of strong rebel commanders capable of enforcing discipline on the western front, Chivers wrote.

In a follow-up article on Wednesday, Chivers quoted a fighter who said that rebels know who supports Gaddafi's regime and that when they liberate towns, "we go straightaway to those homes".  

During the looting, rebels seemed to target hospitals and polyclinics. In Rayayinah, windows and doors had been broken at a polyclinic, and an x-ray machine and electrocardiogram machine appeared to be missing. In al-Awaniya, a hospital had suffered similar damage.

A rebel interviewed by HRW said the medical equipment from al-Awaniya and Rayayinah had been moved to Zintan, the de facto headquarters of the rebel movement in the Nafusa, and that the hospital there would now become the central hospital for the region.

Some Libyans in the opposition reacted to news of the Nafusa abuses with dismay, while others said the repression inflicted by the Gaddafi regime far outweighed the rebels' mistakes.

Ahmed Sanalla, a vocal British-Libyan activist who had been studying medicine in Benghazi when the uprising broke out, told Al Jazeera he found the abuses "disgusting" and that those responsible needed to be brought to justice.

"We are working hard to win the hearts and minds of Gaddafi loyalists, and that's not the way to go about it," he said.

Aisha Mansurey,  an expatriate Libyan activist, called the incidents "unacceptable" and said "measures should be taken to prevent them from happening again."

"Although our freedom fighters are not perfect, they are much more morally conscious than the Gaddafi regime," she said. "It is clear that these incidents are the exception rather than the rule and certainly don't carry official sanction as Gaddafi's atrocities do."

Resentment toward Gaddafi's loyalists among many Libyans is understandable, given the repression, torture and murder attributed to the regime during its 42 years in power. And since the conflict in Libya began in mid-February, loyalist troops have been accused of crimes both worse and more widespread: rape, using landmines, killing hudreds of peaceful protesters, and indiscriminately shelling civilian areas.

But opposition forces have also been accused of committing some of the same acts in limited circumstances: Videos have surfaced of mob lynchings during the early days of the uprising, and rebels have fired rockets and mortars into Gaddafi-held towns without regard to civilians.

Particularly unnerving in the Nafusa are the reports of civilians fleeing before the rebel advance. In the east, by all appearances, the uprising has been greeted by almost the entire population, long overlooked by the Tripoli-based regime.

In the west, however, the rebellion has been limited to Misurata and the Nafusa, and in the mountains, the rebels may be encountering their first taste of engrained regime loyalty. Some towns are even reported to still fly the green flag of the Gaddafi regime after they have been overtaken by rebels. 

Badees, a member of the rebel media committee in the Nafusa town of Jadu, told Al Jazeera that some of the abuse could be attributed to living 42 years under Gaddafi with an "absence of law and no constitution".

"The leadership take the situation seriously this time," he said. "Especially [with] what happend in Qawalish."

Follow Evan Hill on Twitter: @evanchill