Rega said it had asked Swiss prosecutors to investigate, but believed its staff were not involved.
The ex-F1 champion suffered a head injury in a skiing accident last December and was moved to a Swiss hospital last month.
His records were allegedly stolen and offered for sale to several newspapers.
Schumacher, 45, was transferred on 16 June from a hospital in the French city of Grenoble to Lausanne in Switzerland.
His medical documents were shared with the medical and rescue teams involved in planning his move, including Rega.
Schumacher's manager, Sabine Kehm, said last month that the F1 ex-champion's medical files had been "clearly stolen" and were being offered for sale.
The records were apparently being offered to media across Europe for 50,000 euros (Â£40,000, $68,000).
Ms Kehm warned that criminal charges would be pressed if such "confidential files" were bought or published.
On Monday, French police said they had tracked down the IP address of a computer used to share his medical records to a Swiss helicopter firm.
In a statement in French, Rega said it had "found itself at the centre of speculation" as a result of revelations published by French daily Dauphine Libere that the information was sent from one of the computers of an "important helicopter company based in Zurich".
It had filed a complaint with prosecutors in Zurich to ensure "absolute clarity" in this case, it said.
"Rega has no evidence that any of its employees failed in this regard. At this stage, we assume that the rights of the patient to medical confidentiality have been preserved."
The company also said it had no knowledge of the ongoing inquiries being conducted by the authorities.
Michael Schumacher retired from racing in 2012 after a 19-year career.
The investigation into his accident at the Meribel resort on 29 December said he had been skiing off-piste when he fell and hit a rock.
He had been going at the speed of "a very good skier" at the time, they said.
His family has said very little about his medical progress, preferring to avoid the gaze of the international media.
A Swiss air rescue service has lodged a legal complaint after its computer was apparently linked to a bid to sell Michael Schumacher's medical file.