A crackdown overseen by Sisi against supporters of his predecessor Mohamed Morsi has left hundreds dead since the then army chief toppled the Islamist in July 2013.
Thousands of Morsi backers have also been imprisoned, and dozens sentenced to death after speedy trials which the United Nations says is "unprecedented in recent history".
Several youth activists who spearheaded the 2011 revolt against former autocratic president Hosni Mubarak are also serving jail terms for protesting illegally.
"Nobody is against human rights... but today Egypt is in an exceptional condition... is it possible that there will be no violations?" asked Sisi.
"There will be violations. But do we approve them? No," he said in an address to police officers and ministers ahead of the annual police day on January 25.
On police day in 2011, millions launched protests against Mubarak, expressing their anger against the then reviled police force.
Since Morsi's ouster, the police have been back on the streets in full force amid accusations that Sisi's regime is even more authoritarian than that of Mubarak, who quit after an 18-day uprising.
Sisi has repeatedly said that ensuring stability in politically tumultuous Egypt is a top priority rather than promoting democratic freedoms.
Signup to our newsletter and follow us on Facebook and Twitter!
"I am more concerned for human rights than any one else," said Sisi, after awarding families of police officers killed in security operations.
"But come see millions of families... the modest Egyptians who live in regions that need to be improved. What about their rights?"
Sisi defended an ongoing security operation on the unrest roiled Sinai Peninsula, where he said 208 militants have been killed by the security forces in more than a year.
The president said 955 people had been arrested in the region, which borders Israel, but more than half had been released.
"These figures show that...we make sure that innocent people are not killed," he said, adding that the situation in Sinai would take a while to resolve.
Jihadists have stepped up attacks against security forces on the peninsula since the ouster of Morsi.
They say their attacks are in retaliation to the government crackdown against Morsi supporters.
Officials say militants have killed scores of policemen and soldiers in Sinai and other parts of the country.