Two-time world champion, Alonso, drove a brilliant race in the rain in Malaysia to leap to the top of the drivers' standings. That followed his fifth place finish at the season opener in Melbourne.
Fry attributed the team's unexpected success -- after underwhelming performances in qualifying -- to a combination of good driving from Alonso, particularly in Melbourne, and weather conditions in Malaysia, which worked in their favour.
But he said there was still room for improvement.
"From quite early on in testing, we realised we had quite a few issues we needed to sort out. Everyone at the factory has been working hard at that, as we still have a long way to go," Fry said on the Ferrari team web site.
"I think our dry qualifying performance is still around eight-tenths (of a second) off the best while we want to be the best ourselves. Damp low grip conditions suit our car and flatter some of the issues we have with the F2012 at the moment."
Before the season started, it was suggested that Ferrari was in crisis and that the F2012 car was undriveable.
Fry acknowledged the difficulties, which have been seen in Felipe Massa's performance so far.
"The car is quite difficult to drive and Fernando has managed to get the most out of it, while with Felipe, we have struggled to find the right balance to keep him happy," he added.
"In addition, in Malaysia, we had Felipe on intermediates after the red flag but we had a lot of understeer and so we took the gamble of an additional pit stop which did not work out.
"The fact the tyres were only graining and not worn out was about the only call we got wrong from the pit wall at the last race. It was a set-back for Felipe, one of a few unfortunate circumstances for him."
Meanwhile, Fry said he was surprised at Red Bull's poor start: they have not been able to match McLaren's pace in qualifying and while world champion Sebastian Vettel finished second in Melbourne, he failed to make it into the points at Sepang.
Mark Webber has had a couple of unspectacular fourth-place finishes.