Mubarak, 83, is detained in a hospital in the Red Sea resort of Sharm el-Sheikh after officials said he had heart problems.
His wife, Suzanne, who also fell ill when ordered detained, was freed on Tuesday after giving up assets but faces a graft probe.
The timing of their respective illnesses, which meant neither joined other top officials in jail, has fuelled talk that they were getting special treatment by the military.
"The Supreme Council of the Armed Forces affirms that there is absolutely no truth in what was published by the media about the council moving to pardon the former president Hosni Mubarak and his family," it said in a communique on its Facebook page.
The council "does not intervene in any way in legal matters and particularly in holding to account symbols of the previous regime", it said, adding that legal steps were for the judiciary to handle and such "rumours" were aimed at dividing the nation.
As well as being the commander of the armed forces in his capacity as president, Mubarak was a decorated officer who led the air force during the 1973 war with Israel.
Some analysts say the military council, led by Field Marshal Mohamed Hussein Tantawi who served as Mubarak's defence minister for two decades, has been reluctant to humiliate their former leader by putting him behind bars.
But the council has been under public pressure to hold Mubarak and others to account, following a series of mass demonstrations after his ouster on Feb. 11.
Mubarak is being probed for abuse of power, embezzlement and for his role in the deaths of protesters during the 18 days of unrest that led to his overthrow. His wife is accused of using her husband's influence for unlawful personal gain.
Both deny the charges, due to sudden illnesses, neither spent time in prison for questioning despite being ordered detained. Their two sons, Gamal and Alaa, were moved to jail with other top officials and are being probed over corruption and other charges.