The four-time World Champion believes that Ron Dennis always favours one driver within the Woking team and therefore any attempt to create equality is bound to fail.
The former McLaren driver has first-hand knowledge of the inner-workings of the team having driven for them between 1984 and 1989.
And the Frenchman's spat with Ayrton Senna whilst with McLaren is the stuff of F1 folklore.
"I think Ron Dennis is living an involuntary situation that has gone out of his control," Prost told Autosprint.
"His problem, however, is that he's always had a tendency to sympathise more for one of the drivers of his team, for whom his protective attitude emerges. It was like that with Senna, with (Mika) Hakkinen, and now with (Lewis) Hamilton.
"That's the way he is, but this doesn't necessarily end up with technical advantages for his preferred driver. It's simply his way to behave, to communicate his sympathy towards a driver.
And Prost points out that Fernando Alonso has demurred to Dennis' favouritism towards his team-mate.
"I think the reason why Alonso's mood has progressively worsened is that he is not the one at the receiving end of Dennis's sympathies.
"Ron Dennis has made a fundamental error in not having established the hierarchy beforehand. He should have hired Alonso in the role of number one driver in a clear and indisputable way, and have Hamilton racing after having told him he would have been the number two driver."
The 52-year-old also says the Spaniard would have won the title by now - had he been installed as the team's premier driver.
"Probably Alonso would have won the championship this year and, in 2008, Hamilton would have appreciated this situation that would have allowed him to mature with no pressure. And all the problems they have now would have been avoided. By contrast, everything is a lot more complicated now.
"Nowadays I think the future of every F1 team is to have well-defined hierarchies among the drivers. It's sad for the competition, for the sport and for the show, but this is the direction things seem to have taken.
"Alonso has exaggerated a bit with the criticisms and the way he's done it, but everything starts from Dennis's will to always convince his drivers that inside his team there is a situation of perfect technical equality.
"That's something difficult to demonstrate and keep up with at all times, and it can't be restricted to the way the car is prepared.
"There are other aspects: human and psychological elements, which can't possibly end up in a situation of absolute equality. Alonso's problems start from there."
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