The statement from his office came as dozens of demonstrators gathered outside Cairo police headquarters chanting: "The interior ministry are thugs," after an officer killed a driver over a fare dispute.
Earlier on Friday, the interior ministry announced that the policeman, who was badly beaten by a crowd after the killing, had been arrested in hospital.
Police have been on the defensive after a string of deaths in custody over the past year, redolent of the abuses that fuelled an 18-day uprising which ousted president Hosni Mubarak in 2011.
"These actions must be stopped and the perpetrators held to account," Sisi told Interior Minister Magdy Abdel Gaffar, according to the statement.
"This may require some legal amendments, or new laws, that regulate police performance on the street, and that ensure all who violate the rights of citizens will be held to account."
Sisi will present the amendments to parliament within 15 days.
Before marching to Cairo police headquarters, hundreds of mourners turned out for the funeral of the driver, Mohamed Ali Sayed Ismail.
Outside the headquarters, a neighbour of the slain driver accused the government of allowing police to do as they wish.
"We are here because next time it will be our turn, each one of us. (Ismail) was a young respectful man just trying to make a living," said the protester, who gave his name only as Tarek.
"The government has given police a free hand. A dog has more value than Egyptian citizens."
'Egyptian lives matter'
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Ismail's killing sparked fury on social media, coming after a series of deaths in detention and accusations of police involvement in the torture killing of Italian PhD student Guilio Regeni.
"Do we need an 'Egyptian lives matter' campaign again?" asked one prominent Egyptian blogger, who goes by the name Zeinobia.
The interior ministry had all but collapsed during the uprising against Mubarak, with protesters ransacking police stations across the country.
But it had regained popularity after the overthrow of Islamist president Mohamed Morsi in 2013, even as it carried out a deadly crackdown on Islamists that killed hundreds of protesters.
Scores of policemen have been killed in attacks since, and the Egyptian media has been reluctant to criticise the force.
Sisi, who as army chief led Morsi's ouster, won a presidential election the following year.
He has support among the many Egyptians who say the country needs a firm leader, but he has also faced mounting criticism over police abuses and crackdowns on dissidents.
Over the past year, several policeman have been detained for violence against prisoners, and some have been given jail sentences.
Last week, thousands of doctors held a protest against the police after officers allegedly assaulted two doctors in a hospital.
Police have also been on the defensive after the Italian student Regeni was found dead in Cairo on February 3 bearing signs of brutal torture a week after his disappearance in the capital.
Italian media have reported suspicions that he was killed by Egyptian security services. The interior ministry said it was not involved and was investigating his death.