An army doctor has been acquitted of carrying out forced "virginity tests" on female protesters in Egypt last year, dealing a blow to activists and the women at the centre of the case.

Ahmed Adel was found not guilty of public indecency by a military court in Cairo. He was accused of performing the tests on seven women at a military prison who had been arrested in Tahrir Square on 9 March 2011.

The presiding judge said there had been contradictions in the witness testimonies of the three women who came forward.

The first woman to file charges, Samira Ibrahim, was outside court when the verdict was announced. Visibly upset, she joined others in chanting against military rule. She later said on Twitter: "Nobody assaulted my honour. It was Egypt's honour that was assaulted and I will keep going till the very end to regain its rights."

Adel was charged with public indecency and disobeying military orders. After the verdict he told the press that the case was only brought against him because of pressure from the media and foreign organisations such as Amnesty International and Freedom House, whose motives he questioned.

Soha Abdel-Aty, the assistant director of the Egyptian Initiative for Personal Rights (EIPR), which represents Ibrahim, told the Guardian she had no expectation of justice and no faith in a military court, as it was not independent.

"This is entirely a show to convince public opinion an investigation was conducted. The whole sham started out with the fact that the military prosecutor decided to bring this doctor to court with an accusation that did not fit the bill," she said. The charges referred to the conducting of a medical examination in an open space, and thus the allegation of the "virginity tests" was never even acknowledged, she said.

Maj Gen Adel al-Mursi, the head of the military prosecution, defended the verdict in a statement carried by Egypt's official news agency. He said the judge ruled "according to his conscience and in view of the case's documents".

A march to Cairo's high court has been called for Friday 16 March, to coincide with Egyptian women's day.

In December, Ibrahim won a case at the Cairo administrative courts that virginity tests were illegal. It was seen as a victory for the women involved and encouraged others to come forward. Straight after that ruling, it was announced that Adel would face a military trial.

EIPR had initially filed a complaint to the public prosecutor, who referred it to the military justice system. There is no appeals process in military trials and no criminal liability can now be pursued in a civilian court.

Last June, a military general admitted in a meeting with Amnesty International that virginity tests had taken place. Maj Gen Abdel-Fatah El-Sisi, a member of Egypt's Supreme Council of the Armed Forces and head of military intelligence, said the tests had been conducted to protect the military from any allegations of rape, and that they would not happen again.

"The military justice system is very confined in Egypt," Abdel-Aty said. "We have very little access to it and because the crime took place in a military prison, it falls under the jurisdiction of military law."

Another Egyptian general also admitted the examinations had taken place and defended them in an anonymous interview with CNN. "The girls who were detained were not like your daughter or mine," he said. "These were girls who had camped out in tents with male protesters in Tahrir Square, and we found … molotov cocktails and [drugs]."

The women were detained on 9 March, nearly a month after the revolution that forced Hosni Mubarak from power, when soldiers cleared Tahrir Square after men in civilian clothes attacked protesters.

One of the female victims, Salwa Hosseini, 20, told Amnesty she and the other women were forced to undress before being strip-searched by a female guard. Male soldiers looked into the room, and took pictures, she said. EIPR is looking at pursuing the case at the African Commission on Human and People's Rights, which is a semi-judicial body that has weighed a number of cases brought against the Egyptian government.