"We do not give lessons without taking account of the context," Macron said at a press conference with Sisi in Paris, voicing support for Egypt's "fight against violent religious fundamentalism".
France sees Sisi, a former general who ousted the elected Islamist president Mohamed Morsi in 2013, as a key ally in the fight against terrorism and a source of stability in the war- wracked Middle East.
Macron told the press conference that combating extremism "should be carried out with the respect of the rule of law and human rights" and his aides said he raised cases of arrested activists in private during the two-hour talks.
But neither Macron nor Sisi could escape questions over Egypt's record of abuses and repression.
Asked by a French reporter about allegations that an Italian researcher found murdered in Egypt in 2016 died at the hands of the police, Sisi said emphatically: "We do not practise torture."
Egypt is also a major buyer of French arms.