Frederic Cuvillier said he was "determined to obtain the necessary clarifications on the veracity of the allegations that pilots are discouraged from reporting incidents".
On Monday, Britain's Channel 4 aired a programme in which some of Ryanair's staff raised fears over its fuel policy and highlighted three occasions in which pilots called in emergency alerts because they were low on fuel.
Ryanair countered by saying it would sue the broadcaster for defamation, maintaining that bad weather was the cause of the incidents and that its aircraft fully complied with EU regulation.
The documentary cited a survey by a group called the Ryanair Pilot Group, which stated that 94 percent of its members wanted regulators to conduct an inquiry into the safety policies of the low-cost airline.
The survey was conducted in response to a memo sent by Ryanair to pilots which the RPG claims threatened disciplinary action if pilots did not submit their safety reports exclusively to Ryanair and/or the safety regulator.
"Such practices, if they are confirmed, are concerning and would be a violation of applicable rules," Cuvillier said in the statement.
Ryanair dismissed the survey a "fabrication" in a statement, and said the RPG was a front for the European Cockpit Association, a group of pilot trade unions active at its competitors.
The group behind the study "lacks any independence, objectivity or reliability" and did not have access to its more than 3,000 pilots.
Ryanair insisted the survey was part of ECA's 25-year battle to win union recognition at the airline.
All European carriers are obliged to follow security and safety regulations as set out by the European Aviation Safety Authority.
"Ryanair, like other companies, is subject to strict controls, which to this day have not revealed any particular breaches of regulations by this company," Cuvillier said
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The budget airline, meanwhile, has fired Captain John Goss, a 27-year-veteran of the company, for "gross misconduct," it was announced on Thursday, after he appeared in Monday's documentary.
“We will not allow a Ryanair employee to defame our safety on national television just three weeks after he confirmed in writing to Ryanair that he had no concerns with safety," a statement from the Irish airline said.
"We look forward to correcting Mr Goss’s defamatory claims in court in due course," the statement added.