The FIA announced on Friday that Red Bull will be fined $7 million and have their aerodynamic testing time reduced by 10% over the next 12 months.
Red Bull boss Christian Horner was not happy with the penalty, calling it "draconian", as he claimed there were mitigating circumstances.
Meanwhile, Mekies wanted to see a much stronger response from the FIA, as he doesn't believe the penalty will affect Red Bull much at all.
"We have talked a lot in recent weeks about what one can do with half a million more, or a million or two or three," said Mekies, as quoted by Motorsport.com. "Two million [euros] is a significant amount and we have given our opinion several times on this topic.
"We at Ferrari think that this amount is worth around a couple of tenths [per lap] and so it's easy to understand that these figures can have a real impact on the outcome of the races, and maybe even a championship."
He added: "As for the penalty, we are not happy with it, for two important reasons. The first is that we at Ferrari do not understand how the 10% reduction of the ATR can correspond to the same amount of lap time that we mentioned earlier.
"Furthermore, there is another problem in that. Since there is no cost cap reduction in the penalty, the basic effect is to push the competitor to spend the money elsewhere.
"It has total freedom to use the money it can no longer spend on use of the wind tunnel and CFD due to the 10% reduction, on reducing the weight of the car, or who knows what else.
"Our concern is that the combination of these two factors means the real effect of the penalty is very limited."