In a televised address to the nation, Sisi promised to work toward "reconciliation" but not with those who have "shed blood".
Sisi ousted Islamist president Mohamed Morsi last July, since when authorities have crushed his Muslim Brotherhood movement, jailed its leaders and put them on trial.
Sisi said there will be "no leniency and truce with those who resort to violence".
"I am looking to a new era built on reconciliation and tolerance.. Except with those who committed crimes or used violence as a tool," he said.
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