Raikkonen, the 2007 world champion with Ferrari, won last weekend's Australian season-opener from seventh place on the starting grid after managing the tyres beautifully and doing one less stop than his closest rivals.
The Finn was fastest again in free practice for the Malaysian Grand Prix on Friday with Grosjean 10th and sixth in the two sessions at Sepang.
Allison told reporters afterwards that Grosjean was at a disadvantage because he did not have the same package as Raikkonen.
"He's not had an easy weekend either here or there (Australia), because we haven't been able to provide two cars in exactly the same configuration on either occasions," said Allison.
"In Melbourne on Friday he was running a step behind Kimi in terms of his aero package, and then he had the upgrade for Saturday morning but then Saturday was disturbed by the weather. Here, once again, we only have one set of (new) kit and we've chosen to run that with Kimi and Romain is disadvantaged for that."
Allison blamed the situation on Formula One regulations forbidding testing during the season, leaving all upgrades to be tested on race weekends.
"You try to upgrade the cars as fast as you can and generally speaking, that means that you're always going to have one set of kit ahead of the second set and that almost inevitably means that one driver gets to try it before there is a second one available," he added.
"We will always try to get two sets available but it's not always possible. So he (Grosjean) has had a difficult set of circumstances and he's also up against a team mate who is really firing on all cylinders so those are the two things."
Allison said a combination of patience and a good car had helped Raikkonen, who made his comeback last season after two years out, regain his form of old.
"He's certainly very, very relaxed and confident this year. He drove the race incredibly patiently. I think he knew he had a good car under him," Allison said of Melbourne.
"He knew he didn't have to scamper up behind the group in front and he looked after the tyres, only going quickly when he needed to. It was just a very mature and smooth, fast race."
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