"Rega has no proof that one of its employees is implicated," the Zurich-based company, which specialises in emergency medical assistance, said in a statement.
"But out of a concern for absolute clarity in this case, Rega today lodged a complaint against an unknown person with the prosecutor of Zurich canton."
Schumacher, who suffered severe head injuries in a year-end ski accident in the French Alps, was transferred under a pseudonym from Grenoble hospital to University Hospital of Lausanne (CHUV) on June 16 after emerging from a coma.
The 45-year-old German was taken by ambulance but Rega was also contacted when helicopter transport was being considered.
The French daily "Le Dauphine Libere" reported on Monday that leaked documents being offered to European media for some 60,000 Swiss francs (39231.14 pounds) appeared to have come from the IP address of a computer at a Zurich-based helicopter company.
Rega said it had no evidence that any of its employees violated patient privacy and medical secrecy after receiving Schumacher's medical report from the Grenoble hospital.
Noting that it was now at the "centre of speculation", Rega said it was making a public statement to clarify the situation following the French newspaper report.
A spokeswoman for the Zurich cantonal prosecutor confirmed the Rega complaint had been received, but said it had not opened a formal investigation for now. The prosecutor was in talks with French authorities regarding jurisdiction, she said.
Schumacher's agent Sabine Kehm said last month that medical records purported to be his had been offered for sale and officials were investigating the theft.
Criminal charges and damages would be sought against anyone involved in the illegal sale or publication of his confidential records, she said at the time. Kehm, contacted by email on Tuesday, said she had no further comment at this stage.
Swiss and German newspapers have reported that Schumacher was semi-conscious during the ambulance trip and able to communicate by nodding his head.
Experts at the CHUV neurological rehabilitation unit stimulate patients at its "Jardin des Sens" or Garden of the Senses by exposing them to water, scents and other elements. The area has been cordoned off to prevent media access.
Schumacher, the most successful Formula One driver of all time, has had several brain operations since his accident in the resort of Meribel and is expected to face a long recovery.
His wife Corinna and teenage daughter and son live in the family home midway between Geneva and Lausanne.($1 = 0.8926 Swiss Francs)
(Reporting by Stephanie Nebehay in Geneva; additional reporting by Joshua Franklin in Zurich; editing by Alan Baldwin)
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