Dr. Ahmed Adel was cleared because the judge found contradictions in witness statements, Mena news agency said.
The case was brought by one of the women, Samira Ibrahim, who said the “tests” took place after they had been detained during protests last year.
Demonstrators are gathering to protest the ruling.
The practice drew an outcry after Samira Ibrahim and other women spoke out about their treatment following their arrest during a protest in Tahrir Square in March 2011 – weeks after the fall of President Hosni Mubarak.
They said they were forced by the Egyptian army, while in detention, to submit to a five-minute-long so-called virginity test by a male doctor.
The army initially denied such tests had taken place, but a senior general, speaking anonymously, later admitted that they had happened.
Samira Ibrahim launched a legal challenge to prevent such tests happening again, and Cairo’s administrative court eventually ruled that the tests were illegal.
But the woman said, before the trial of Ahmed Adel, that witnesses she hoped would speak in her defense had changed their story at the last minute.
According to Mena news agency, the judge said he made the ruling “from what has been proven in documents and based on my conscience,” adding that he had “not been subjected to any pressures”.
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