Bassem Youssef rose to fame after the uprising that swept Hosni Mubarak from power in 2011, with a satirical online show. His programme, that has been compared to the Daily Show of US satirist Jon Stewart, is now broadcast on Egyptian TV.
The comedian is accused, among other things, of undermining the standing of Islamist President Mohamed Mursi. The prosecutor general issued an arrest warrant for him on Saturday after at least four legal complaints filed by Mursi supporters.
An official in the prosecutor general's office confirmed that questioning had begun. Youssef voluntarily showed up at the prosecutor general's office on Sunday, so as to avoid arrest.
He was wearing an oversized version of a graduation hat modelled on one donned by the president when he was awarded an honorary degree in Pakistan earlier in March.
Youssef has worn the hat on his widely-watched show, one of many satirical jabs at the president. Last year, he poked fun of Mursi's repeated use of the word "love" by singing a love song to a red pillow with the president's face printed on it.
The questioning of the comedian has raised fears over freedom expression in the post-Mubarak Egypt.
"It is an escalation in an attempt to restrict space for critical expression," said Heba Morayef, Egypt director at Human Rights Watch.
Prominent liberal politician Mohamed ElBaradei said it was the kind actions only seen in "fascist regimes". "It is the continuation of the failed and ugly moves to thwart the revolution," he said.
Youssef's questioning came after the prosecutor general issued five arrest warrants for prominent political activists accused of inciting violence against the Muslim Brotherhood, the group that propelled Mursi to power in last year's election.
The prosecutor's office has also summoned several other prominent media figures for questioning over accusations they insulted the president.
Opposition figures say the prosecutor, Talaat Ibrahim, is biased towards Mursi, who appointed him last November, and they want him removed from office.
A court ruled last week that Ibrahim's appointment was illegal and that he must step down. Ibrahim, who denies any bias, plans to appeal the ruling.