Egypt's president, Mohamed Morsi, has promoted several generals in a show of untrammelled support for the embattled military, who have been strongly condemned after this week's leak of a top-level investigation that made damning allegations of malpractice.

Officers allegedly killed, tortured and abducted Egyptians during the 2011 uprising, according to the investigation commissioned by Morsi last year. The suppressed report, sections of which have been obtained by the Guardian, also alleged that senior army doctors were ordered to operate without anaesthetic on wounded protesters at a military hospital in Cairo during protests against military rule in May 2012.

The seriousness of the allegations has led to demands for Morsi, Egypt's first elected civilian president, to bring the officers responsible to account. But such a move would risk outraging the army, with whom Morsi has a delicate relationship.

Standing alongside members of the Supreme Council of the Armed Forces, who ruled Egypt between the removal of Hosni Mubarak and Morsi's election, the president said: "Any insult against the armed forces is an insult against all of us, and we reject any kind of insults … I announce this to the whole world: we appreciate the great role that the armed forces has been playing in maintaining the safety and security of this country."

Morsi promoted three major-generals to the honorific titles of lieutenant-general. He listened attentively as the head of the armed forces, General Abdel Fattah al-Sisi, denied any accusations of military malpractice. "The armed forces during the last two years was very, very fond of Egypt and the people of Egypt and did not commit any malpractices whatsoever," Sisi said. "By God I swear that the army, since 25 January 2011, did not kill and did not order to kill, did not deceive and did not order to deceive."

Morsi may be at pains to placate the armed forces because of cryptic statements by Sisi recently about the direction in which the country was heading. In February Sisi opaquely warned that ongoing political turmoil in Egypt "could lead to the collapse of state". This prompted fears that the army had not entirely rejected the idea of taking a more active role in the running of the state.

Elijah Zarwan, a Cairo-based analyst, said: "It's very important for the president to keep the military – who are an important centre of power – happy."

It is thought that last autumn Morsi agreed a deal with senior generals to refrain from meddling in military affairs in exchange for their support. Analysts cite a clause in Egypt's new constitution that granted the military the right to try civilians in army courts – a major concession that suggested Morsi was not willing to confront army interests.

But this week's allegations about the army will have made generals fear that Morsi might at some point have to break his promise and investigate senior officers to satisfy public opinion. In some quarters there was even the suggestion that the president's office leaked the documents itself to discredit the army.

Additionally, the admission of Morsi's nephew to a military training academy last month will have riled many officers, who do not want the army to fall under the influence of associates of the Muslim Brotherhood, the Islamist group to which Morsi is allied.

"The choice of Morsi's nephew is obviously meant to send a message that the Brotherhood is moving in on the military," Professor Robert Springborg, an expert on the Egyptian military at California's Naval Postgraduate School, told the Guardian last month. "There is going to be dissatisfaction of a very major sort about this."

Springborg said certain sections of the military were deeply dissatisfied with the direction the country was heading. "It's clear that the economic situation is going to greatly deteriorate. It's clear that you're not going to have political stability any time soon.

"So against that backdrop of the lack of the capacity of the Brotherhood to govern, and its threat to the military itself, I just say to myself: … there are people within that military who are going to react. Much as they don't want to step into the breach, I think they fear the alternative yet more."

Morsi will also be wary of taking on the military wrongdoing for fear of drawing attention to allegations of security sector malpractice during his own tenure.

But indifference to the findings was not limited to Morsi alone. The reaction from parts of the opposition was also limited, partly because the military are seen as a lesser evil than the Brotherhood – and in some quarters even an ally. "They don't want this fight now," said Michael W Hanna, an Egypt analyst at the Century Foundation. "Some among the opposition see the military as a potential curb on the Brothers and some – though not the leadership – might go as far as to say that the military might be the best path to follow in the future."

Morsi's own reaction may placate the army for now, but it will deeply disappoint rights campaigners, who hoped that the findings of the report that he himself commissioned would be taken seriously. Earlier in the week, campaigners told the Guardian they hoped the leaked report would now be published officially by the president to give it the impact it deserved. "This report needs to be made public by the president," said Heba Morayef, the Egypt director of Human Rights Watch. "It needs to be published so that it can have that official stamp of endorsement." But following Morsi's reaction on Thursday, that endorsement now looks unlikely.