The first doctor to be brought to trial in Egypt on charges of female genital mutilation (FGM) has been acquitted, crushing hopes that the landmark verdict would discourage Egyptian doctors from conducting the endemic practice.

Raslan Fadl, a doctor and Islamic preacher in the village of Agga, northern Egypt, was acquitted of mutilating Sohair al-Bata’a in June 2013. The 12-year-old died during the alleged procedure, but Fadl was also acquitted of her manslaughter.

No reason was given by the judge, with the verdict being simply scrawled in a court ledger, rather than being announced in the Agga courtroom.

Sohair’s father, Mohamed al-Bata’a, was also acquitted of responsibility. Police and health officials testified that the child’s parents had admitted taking their daughter to Fadl’s clinic for the procedure.

Despite his acquittal, the doctor was ordered to pay 5,001 Egyptian pounds (about £450) to Sohair’s mother for her daughter’s manslaughter, after the pair reached an out-of-court settlement.

The case was pursued rigorously by activists and state officials in the hope that it would send a strong message to doctors that FGM, which was nominally made illegal in 2008, will no longer be tolerated in Egypt. Instead, said a lawyer from a local rights group – the first to take up Sohair’s case – the verdict signalled the opposite.

“Of course there will be no stopping any doctor after this. Any doctor can do any FGM he wants now,” said Atef Aboelenein, a lawyer for the Women’s Centre for Guidance and Legal Awareness, who was the first to find out the verdict.

Interviewed in his clinic hours after the verdict, Fadl admitted he had removed a wart from Sohair’s pubic area. But the doctor said his incision was minor; claimed she died from an allergic reaction to penicillin; and denied he had ever carried out FGM – a practice he said was against religious teaching, and which he claimed he had always refused to do.

“The incision was just 1cm wide,” Fadl said. “Do you know what 1cm looks like? Do you know how small that is? In every country in the world you would carry out this operation.”

Fadl said his accusers were “on drugs”, and asked “those human rights activists to come to me and I will teach them about human rights. They’re letting the Palestinians be slaughtered, and instead they’re going after me?”

The lawyer who pushed for Fadl’s prosecution, Reda al-Danbouki, said the verdict contradicted the evidence presented in court. Though Fadl denied committing FGM, a report prepared by Egypt’s forensic authority “proved what happened in the genital area of the girl was a clear circumcision operation”, Danbouki claimed.

Suad Abu-Dayyeh, regional representative for Equality Now, an international group that campaigned on the case, said: “It’s a very unjust verdict from the judge. It sends a very negative message. It was the first case in the country and we were hoping we could build on it.”

Outrage was harder to find in Fadl’s village, where both FGM and the doctor have stronger support. “I’m very happy for him,” said one young woman waiting in Fadl’s clinic. “It wasn’t his fault.”

According to surveys by Unicef, an estimated 91% of married Egyptian women aged between 15 and 49 have been subjected to FGM, 72% of them by doctors. Unicef’s research suggests support for the practice is gradually falling: 63% of women in the same age bracket supported it in 2008, compared with 82% in 1995.

But in rural areas with a low standard of education, such as Sohair’s village of Diyarb Bektaris, FGM still attracts instinctive support from Muslims and Christians, who believe it decreases women’s appetite for adultery. Residents of the village say they can easily find doctors willing to operate on girls for around 200 Egyptian pounds, and that it will take more than a court case to stop them seeking the operation.

“We circumcise all our children – they say it’s good for our girls,” Naga Shawky, a 40-year-old housewife, told the Guardian earlier this year. “The law won’t stop anything – the villagers will carry on. Our grandfathers did it and so shall we.”

Mostafa, a 65-year-old farmer, said he did not realise that FGM had been banned. “All the girls get circumcised. Is that not what’s supposed to happen?” he asked. “Our two daughters are circumcised. They’re married and when they have daughters we will have them circumcised as well. If you want to ban it properly, you’d have to ban doctors as well.”

Fadl said his experience had caused other doctors to stop committing FGM so openly, but that they still did it in secret. “A lot of people got scared, so now they’re doing it in their homes.”

After the verdict, a local doctor uninvolved in the case said clinicians would continue carry out FGM undeterred. “They will do whatever they want when they want without worrying about anything,” said Dr Ahmed al-Mashady, who stressed he did not personally engage in FGM. “They must keep doing this because it’s a protection for the girl. Religiously it’s a good thing.”

While many use Islam to justify FGM, activists stress it is a cultural, rather than a religious practice. FGM is not mentioned in the Qur’an, and the practice is not as prevalent in other predominantly Muslim countries.

Sohair’s father could not be reached for comment. But at Sohair’s home, her great-uncle Mohamed said the family was unaware that the trial had ended. “The verdict was today? Praise God,” he said, before declining to comment further.

In May, Sohair’s grandmother, also named Sohair, admitted to the Guardian that an FGM procedure had occurred, but claimed her death was “what God ordered”.

Equality Now and local lawyers said they would appeal against the verdict, and redouble their efforts to curb the practice. “We will focus all our efforts on cases of FGM and underage marriage,” Aboelenein said.

Activists, however, said it would take more than court cases to end a practice that is so ingrained. Equality Now’s Suad Abu-Dayyeh called for a sustained outreach programme in which campaigners frequently visit Egypt’s rural areas to discuss a topic that has previously never been questioned. “You need to go continuously into the communities. We need to find a way of really debating these issues with the villagers, the doctors and the midwives.”

Additional reporting: Manu Abdo