The Italian team have suffered problems with the correlation of data from the wind tunnel and the results seen at the racetrack.
They are planning to shut down their wind tunnel and use other facilities in order to improve the development of the F2012.
Alonso is trying to fend off a five-strong chasing pack, led by Red Bull's Sebastian Vettel, with just six races of the season remaining.
The Spaniard's advantage is down to 29 points and Ferrari need to respond having been outpaced by McLaren and Red Bull since Alonso's win in Germany on July 22.
That pattern looks set to continue at Suzuka this weekend as Alonso ended practice in fifth place, behind both Red Bulls and the McLaren of Lewis Hamilton.
Ferrari have already been using other wind tunnels in conjunction with their own, but Domenicali believes shutting down their facility is the best solution to the problem.
Domenicali said: "I am sure it has also happened to other teams but I have seen in the second part of the season when trying to bring new updates to the car that not all the updates are working on track. So we started to investigate it more and we found this issue.
"We understood it was possible it was coming from the tool (wind tunnel), that is not really up to the speed of the new technologies that are available on the market.
"That is why we think we need to improve, so that the percentage of what we bring to the track is higher than we have now.
"I think the situation with the championship is very clear; if you are not able to improve the car then it is more difficult to fight for the championship as we cannot rely on the problems of the others. That's a fact but it does not mean we are not working as hard as possible.
"We cannot rely on only being third or fourth, we need to make sure we can win a race and then we will see what is the situation with the others.
"The plan is to bring new developments to every race but it is not easy so the guarantee is it is not impacting on the effort of the team who try to work as hard as possible."
The problem also has the potential to hinder the development of Ferrari's 2013 challenger, and Domenicali believes that adds to the importance of getting the problem sorted as soon as possible.
He said: "I think our structure is not the best one, as always we are trying to improve the quality of tools we have and that is what we are trying to do.
"In order mainly to improve the correlation issue we had and that is the plan that we should be able to do in the next season.
"It is still open and we are working in our wind tunnel and using other facilities, and in the next couple of weeks we will define what is the problem, to be more specific and to see what time we have to spend shutting it down and improving things not at the maximum level at the moment."