Minister Abdel Fatah al-Sissi's remarks follow a report leaked to a British newspaper which implicates the army in serious human rights abuses.
He called the claims a "betrayal".
Over 800 people were killed in violence during and after Egypt's 2011 uprising, but the deaths were widely blamed on the police rather than the army.
A document leaked to the Guardian newspaper which was reportedly presented to President Mohammed Morsi late last year clearly implicates the armed forces in abuses during the 18-day revolution.
On Friday, Human Rights Watch called for the full report into police and military abuses between January 2011 and June 2012 to be made public.
"Victims' families have the right to know the truth about their loved ones' deaths. Even if certain information can't be made public in the interests of justice, all Egyptians need to know what happened," said Nadim Houry, deputy Middle East director at Human Rights Watch.
The leaked chapter contains testimony relating to civilians detained at military checkpoints who were never seen again and reports that the army delivered unidentified bodies to coroners.
The report also presents evidence that protesters from Tahrir Square were detained by the army and tortured inside the nearby Egyptian Museum, before being moved to military prisons.
In a joint press conference with Mr Morsi on Friday, the defence minister said: "I swear to God from the beginning of the 25 January revolution until now, the armed forces did not kill or order killing, did not betray or order betrayal, and did not commit treason or order treason."
Mr Sissi called on the public to consider that "the armed forces are honourable, faithful and nationalistic" before they "betray your army".
Over recent weeks, members of the committee that compiled the report, which included human rights lawyers, had said that the military had not been co-operative during the investigation.
Egypt's defence minister has denied claims that the armed forces were involved in killing and torturing protesters during Egypt's revolution.