At the conclusion of a meeting between President Mohamed Morsi and Egypt's Supreme Council for the Armed Forces (SCAF), the president promoted several top officers in an effort to thaw the recently strained relationship between the army and presidency.

Rumours in February that Abdel-Fattah El-Sisi was about to be dismissed from his post as defence minister by Morsi's government were categorically denied by El-Sisi afterwards.

The rumour had brought sharp responses from military officers, who warned of attempts to place Muslim Brotherhood members or associates in key military positions. El-Sisi himself implied this would fail in a speech delivered in March.

The president on Thursday promoted the commanders of three branches of the military – the air force, navy and air defence forces – from major-generals to lieutenant-generals.

A source close to the meeting told state news agency MENA that President Morsi had stressed his rejection of any attempts to harm the army's image.

A leaked presidential report mentioned by UK daily The Guardian cited brutal human rights violations by army officers and doctors during SCAF's brief rule between the ouster of Hosni Mubarak and Morsi's inauguration as president.

The report, not yet officially published, said doctors in army hospitals were ordered to operate on injured protesters without anaesthesia following clashes between protesters and the military in 2012.

Egypt is undergoing a period of political unrest and economic malaise, manifest through continued protests, often turning violent as the opposition calls for the dismissal of the Morsi-appointed government and prosecutor-general.

An increasing budget deficit and worryingly low levels of foreign reserves are forcing the government to seek foreign loans, the most pressing of which is an IMF loan that the government needs to restore investors' confidence.

Tension between the presidency and army began in late 2012 when the SCAF invited the presidency and opposition forces for national dialogue – a move perceived as a tacit threat of military intervention.

The initiative came following Mori's controversial 22 November constitutional declaration, which temporarily made the president's decisions impervious to judicial oversight.