The suspect, named as Moshe Harel by local press, is accused of organising more than 30 illegal kidney removals and transplants at a clinic near Kosovo's capital Pristina, the prosecutor's office said.
"I will do my utmost so that this person, who, in addition to criminal offences has harmed the international image of Kosovo, is brought to justice for these acts," said Justice Minister Abelard Tahiri on Facebook.
Police announced his arrest in Cyprus last week.
Harel has been hunted by the authorities for almost a decade for exploiting victims, often recruited from poor areas in Eastern Europe and Central Asia, by promising 15,000 euros ($18,000) for their organs.
Recipients, mainly Israelis, would pay up to 100,000 euros for the transplant.
The organ trafficking network came to light in 2008 after a Turkish man collapsed at Pristina airport after having a kidney removed.
Police raided the Medicus clinic, which shut following the scandal.
In 2013, an EU-led court in Kosovo sentenced five Kosovan doctors to up to eight years in prison for organ trafficking in the country.
Donors, whose organs were illegally removed, were left without proper medical care and treated "like waste," prosecutors said at the time of the trial.
But the Supreme Court of Kosovo annulled the verdict in 2016 and ordered a new trial, which is ongoing.
The indictment named Harel as the trafficking network's mastermind, while Turkish doctor Yusuf Ercin Sonmez -- labelled by Kosovo media as the "Turkish Frankenstein" and still on the run -- was suspected of performing the transplants at the clinic.
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