It said that Egypt's Supreme Council of Armed Forces, which assumed control after the 18-day uprising that toppled Mr Mubarak in February, had made only empty promises to improve human rights.
Crackdowns on dissent have claimed numerous lives, including at least 33 people who have been killed in Cairo's Tahrir Square over the past few days as throngs returned to the crucible of the earlier pro-democracy protests.
Amnesty’s report was issued as protestors in the second city of Alexandria reported that tear gas had been fired on from helicopters. The health ministry said 40 people had been injured though students claimed the real number was in the hundreds.
The human rights group said military courts had tried thousands of civilians and emergency law had been extended. Torture had continued in army custody, and there were consistent reports of security forces employing armed "thugs" to attack protesters, it added.
"The SCAF has continued the tradition of repressive rule which the January 25 demonstrators fought so hard to get rid of," said Philip Luther, Amnesty's Middle East and North Africa acting director.
"Those who have challenged or criticise the military council - like demonstrators, journalists, bloggers, striking workers - have been ruthlessly suppressed in an attempt at silencing their voices.“The brutal and heavy-handed response to protests in the last few days bears all the hallmarks of the Mubarak era."With elections due to start next week in doubt, William Hague, the Foreign Secretary, has called on the military ruling council to abandon emergency powers, stop detaining protestors and stop trying civilians in military courts.By August, Amnesty said SCAP had put 12,000 civilians on trial in “grossly unfair” military courts and sentenced at least 13 to death.Charges against demonstrators included "thuggery", "breaking the curfew", "damaging property" and "insulting the army". Allegations of army abuse seemed to have been largely ignored, the report said."Amnesty International found ... that the military council had met few of the commitments it made in its many public statements and had worsened the situation in some areas," the group said.It said journalists and broadcasters had been summoned to military prosecutors an attempt to suppress negative reporting. Military pressure had also led to a number of current affairs television shows being cancelled."The Egyptian military cannot keep using security as an excuse to keep the same old practices that we saw under President Mubarak," said Mr Luther."If there is to be an effective transition to the new Egypt that protesters have been demanding, the SCAF must release their grip on freedom of expression, association and assembly, lift the state of emergency and stop trying civilians in military courts."