We tackle the problem of minimizing the number of aircraft potential conflicts via speed regulations and taking into account uncertainties on aircraft position due to wind and temperature. The resolution is done at a strategic level, before any of the aircraft has departed. Owing to the complexity of this kind of optimisation problem, a simulated annealing metaheuristic approach is employed. A scenario with four hours of traffic overflying the Spanish (structured, continental) airspace has been selected. Inputted traffic provides routes, Mach profiles (considered to be constant), and altitude profiles as in their flight plans. Probabilistic weather forecasts from an Ensemble Prediction System are employed. Solutions provide constant speed profiles that slightly differ from those in the flight plans. It is shown that the number of conflicts can be significantly reduced by slightly modifying flight plan speeds while not altering the routes, nor the altitudes, both selected by the airspace user. The impact of this resolution strategy in flight efficiency is also analyzed.