Franz Tost had defended Toro Rosso's decision to drop both 2011 drivers, saying the team is a place for rookies, not experienced drivers.
Toro Rosso announced earlier this week that both Sebastien Buemi and Jaime Alguersuari had been dropped in favour of Daniel Ricciardo and Jean-Eric Vergne.
The decision came as a shock to many in Formula One, including the two drivers, who believed their places at the team were secure.
However, Tost says the decision to drop the two was always in the pipeline as Toro Rosso is a "rookie training school" and not a place for experienced drivers.
"Sebastien has been with us for three seasons and Jaime for two and a half. Both of them worked hard for the team, doing their very best and achieving some good results," he said.
"However, Scuderia Toro Rosso's ethos has always been that of the "rookie training school" and with over two seasons under your belt, you are no longer a rookie.
"In an ideal world, drivers would move from Scuderia Toro Rosso to Red Bull Racing, but there are no vacancies with our sister team right now.
"It might be seen as a harsh decision, but Formula 1 is a tough environment and Toro Rosso has always been very clear about the principles behind its driver choice."
Tost's comments mean that new signings Ricciardo and Vergne, both Red Bull junior drivers, probably shouldn't get too comfortable either as, after two or three years, they too should expect to get the boot.
But despite the team's policy meaning they will always have young and inexperienced, Tost insists "it's not frustrating, in fact quite the opposite.
"It is a very interesting experience for everyone in the team to work with young drivers and it means you can educate them the way you want.
"Everyone, from the race engineers to the communications people can try and give the new drivers good habits, which they can use for the rest of their career."