Pirelli announced earlier this week that it would be tweaking the constructions of its rubber from next month's Canadian GP in light of the four-stops needed at the Spanish Grand Prix.
With the move expected to benefit those teams like Red Bull and Mercedes that have struggled with the tyres so far this year, Boullier believes that few other competitions would have accepted such a change once a title battle was underway.
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"There aren't many sports where there are such fundamental changes to an essential ingredient part-way through a season," said Boullier on Thursday.
"Just imagine for a moment that, because a football team can't run as fast as its opponent, the dimensions of the pitch are changed at half time!
"That there are changes to come can be seen as somewhat frustrating, and I hope they are not too extreme. It's clear that Pirelli have found themselves in a difficult situation and under pressure from different quarters."
Boullier believes the situation is especially unfair because all outfits had access to Pirelli's 2013 tyre data at the same time - and the move could hurt those outfits that elected to focus their designs on ensuring the tyres were looked after.
"Last year, when we were designing our 2013 car, each team received information from Pirelli and everyone did the best job they could to develop a chassis which would make best use of the tyre characteristics," he said.
"We even ran with some experimental 2013 tyres at the end of last season, to assist us in confirming our development paths.
"As with every season, some teams do a better job than others with their designs, and some drivers are more adaptable than others to the changes of both car and tyre.
"It is frustrating when you've developed a car from a set of tyre specifications which are available to everyone – for tyres that are the same for everyone – to then be told that they are being changed mid-season."
Despite his clear frustration about the situation, which comes as Kimi Raikkonen lies just four points off the lead of the title standings, Boullier has said his staff will simply dig deeper to try and recover any ground it loses.
"We have a team of talented designers and engineers who will be working twice as hard to ensure we adapt to these changes in the most competitive manner," he added.