Sisi, a former general who ousted the elected Islamist president Mohamed Morsi in 2013, will meet the French defence and foreign ministers as well as business groups during his three-day trip that started on Monday.
Macron, a 39-year-old centrist elected in May, is pushing a pragmatic, results-oriented foreign policy but also one that sees France uphold its historic mission of defending human rights.
The visit will be a test of this balancing act because Egypt is a major buyer of French arms and a crucial partner in the war-wracked Middle East. But Sisi is accused of systematic abuses and repression.
"President Macron should refuse to continue France's disgraceful policies of indulgence toward al-Sisi's repressive government," the head of Human Rights Watch in France, Benedicte Jeannerod, said in a statement on Monday.
The New York-based group said France should "stop ignoring serious abuses" and pressure Sisi by making future economic cooperation and military support conditional on improvements in human rights.
At a press conference of various rights groups on Monday in Paris, Amnesty International also urged Macron to speak out about human rights.
"The silence of foreign governments sends a message to the Egyptian authorities that they can continue," said Hussein Baoumi, Egypt expert at Amnesty International.
Asked about the criticism of his rule, Sisi told France 24 "there are no political prisoners in Egypt", insisting all detainees were interrogated and brought before the courts according to normal judicial procedure.
In a separate interview with French daily Le Figaro, the president said he was trying to balance rights with security needs.
"Egypt wishes to achieve the necessary balance between the rights and duties of citizens on the one hand, and the security challenges of the fight against terrorism on the other," he told the paper.
"It's sometimes a difficult equation when your responsibility is the security of a hundred million citizens."
Regarding Islam, Sisi said there needed to be religious discourse to combat extremism.
"We must work together and unite to correct erroneous interpretations of religious precepts erected as ideological pretexts to justify violence and terrorism," he told Le Figaro.
A statement from Macron's office last week said their talks would focus on security and regional stability "but also the human rights situation to which France is particularly attentive".
In one of his first meetings as president, Macron welcomed Russian President Vladimir Putin in May and surprised some observers by speaking out against Russian state propaganda and raising alleged abuses in Chechnya.
But government sources told AFP behind-the-scenes diplomacy would be favoured over any public confrontation with Sisi.
"If we arrive saying 'what you're doing is wrong', it's not effective. What works is bringing up specific cases. We need to be stubborn but discreet," one diplomat told AFP.
Egypt is a major buyer of French military equipment with orders worth more than 5.0 billion euros ($5.8 billion) since 2015 including for 24 Rafale fighter jets.
Those deals were negotiated by former defence minister Jean-Yves Le Drian who is now foreign minister in Macron's government.
Rights groups have repeatedly accused former army chief Sisi of repressive policies that stifle dissent in the media and politics, as well as the use of torture by security forces.
"It's important that he raises it publicly," Mohamed Zarea, vice-president of the FIDH global association of human rights groups, told reporters on Monday as he sounded the alarm about Egyptian NGOs being strangled.
But the most populous country in the Middle East is viewed as a vital partner by Western countries which fear more instability in the war-ravaged region.
US President Donald Trump in April congratulated Sisi on a "fantastic job" during a meeting at the White House. The previous month, German Chancellor Angela Merkel travelled to Cairo to hold talks with the Egyptian leader on stemming migration to Europe.
Sisi's visit to France come as Egypt continues to battle extremist groups that stepped up their attacks after Morsi's ouster.
Sixteen policemen were killed in a shootout with militants on a road 200 kilometres (125 miles) southwest of Cairo at the weekend.
Le Drian sent his condolences and pledged solidarity in "the fight against terrorism".