Fifty-two men were tried in the case, which drew widespread criticism from human rights groups and Western governments.
But the current wave has already surpassed that incident both in numbers and in state action, with defendants facing much faster trials than usual, said Dalia Abd Elhameed, EIPR's gender and women's rights officer.
The man says he later felt going to the police was almost as traumatic as the incident itself.
Police records show officers create false dating profiles and set up dates only to arrest the men who show up.
Many of these cases went to court where the average sentence was around three years in jail, although in some cases it went up to 12.
Sisi has been criticized by the Brotherhood as being anti-Islam, and rights groups say tough treatment of the LGBT community is a way to counter that while diverting attention from the country's tough economic conditions.
The overwhelming majority of those arrested are not involved in the flag case, however, and have simply been arrested over their perceived sexual orientation in the following days.
Police have raided homes, parties, and used online dating apps to lure gay men - a common tactic in Egypt - to arrest most of them, their lawyers say.
At least five such examinations have taken place, Amnesty International says.The crackdown has Egypt's already underground LGBT community living in fear.Five gay men who all requested anonymity said they were avoiding gay-friendly spaces and deleting online dating profiles for fear of arrest. But the recent developments underscore an existing reality for gay Egyptians: they are in constant physical danger. We're not talking about gay rights here, no one is calling for marriage equality, we face the possibility of jail and humiliation for merely existing," said one 25-year-old gay man.Judicial sources do not deny the examinations take place but say they are legally carried out and are not a form of abuse.Egyptian authorities do not deny going after gays and an investigation report provided to Reuters by the Egyptian Initiative for Personal Rights (EIPR) openly refers to the police's campaign on homosexuals.