"We feel that all of these laws should be scrapped in order to have a proper election which allows all voices to be able to surface in an equal manner."
Shetty said military courts in Egypt had tried between 7,000 and 10,000 civilians since Egypt's Supreme Military Council took over power after Mubarak quit on February 11.
Military trials for civilians "are not in line with international fair trial standards," he said, because they are not independent, provide no transparency and the system of defence is limited.
Emergency law, particularly provisions which for decades provided security forces and police great leeway to conduct arrests, "is simply not required," he said, adding that the existing penal code was enough to guarantee public order.
During his visit to Egypt, Shetty met representatives of the interior and foreign ministries as well as rights activists and relatives of those who died in the 18-day popular protests that toppled the Mubarak regime.
"It is essential... to investigate all cases of torture, including by the armed forces," said Shetty, adding that the investigation of recent cases of forced virginity tests against female protesters was an "urgent priority."
Shetty said the toppling of Mubarak's authoritarian regime had paved the way for "significant changes" in Egypt including the release of the majority of political prisoners.
"If you talk to people there is no question it's much freer now to move, there is more media freedom. There is a big change and we have to acknowledge that."
Later he met outgoing Arab League chief and presidential hopeful Amr Mussa, and called on Arab states to act to help end the violence in Syria, where activists say anti-regime protests have killed nearly 1,700 people.
Amnesty puts the number of dead in Syria at at least 1,200.
"I urged the League of Arab states to take far stronger action on the gross human rights violations taking place in Syria," Shetty said after meeting Mussa.
"In contrast to their vocal stance on Libya and support for international action, Arab countries have stayed largely muted on Syria."
On June 18, Mussa said the Arab world was concerned about events in Syria.
"There is a worry in the Arab world and in the region concerning the events in Syria," he told reporters in Cairo.
The Syrian crisis is the subject of "many contacts" between leaders across the region "to exchange points of view," Mussa added.
Shetty said on Saturday Amnesty has called for the situation in Syria to be referred to the International Criminal Court.
"We have documented security forces operating a shoot-to-kill policy against demonstrators -- the vast majority of whom are peaceful -- as well as widespread arbitrary detention and torture, including of children," he said.