FIA president Jean Todt believes the clash of dates between the 2016 Le Mans 24 Hours and inaugural F1 race in Azerbaijan was unavoidable.
Nico Hulkenberg will be unable to defend the Le Mans title he won with Porsche team-mates Nick Tandy and Earl Bamber earlier this year as Baku's first-ever race, the European GP, has been pencilled in for June 19, which is the same date as next year's Le Mans.
World Endurance Championship chief Gerard Neveu was critical of the decision to schedule a Formula 1 race on the weekend of June 18-19, saying it was a "clear attack" on his series.
Although he is "sorry" over the conflict, Todt believes it was only a matter of the time before it happened.
"Organising the calendar is a very tricky job because you have 21 races in Formula 1, 10 races in Formula E, 10 races in World Endurance and 14 [World Championship] rallies," said Todt.
"To make one calendar without any conflict is not possible. But for Le Mans, I'm quite confident. The start [of the grand prix] will be at midday and Le Mans will finish at 3pm.
"Maybe for one or two drivers it does not allow them to do it. I'm sorry to say we cannot do better."