The Spanish squad has kept Marussia in sight so far this season despite being in the middle of a major restructure that includes establishing a new headquarters in Madrid.
HRT driver Pedro de la Rosa suggested on Friday that his team would be better off focusing on its own improvement rather than making beating Marussia a specific target, and Perez-Sala believes John Booth's team is likely to remain a step ahead for now.
"Hope is the last thing to die, and I hope we can finish ahead of them in a race, but we have to be realistic," Perez-Sala told AUTOSPORT.
"They are more competitive than us. They have done a good job and I think short term we have many things to focus on in the building of the team.
"So I don't believe we can be consistently more competitive than them in the short term."
Perez-Sala believes that moving into the new Madrid base, which was unveiled this week, shows that HRT's transformation is making good progress.
"It's a big, important step for us," he said. "Being in Formula 1 is a luxury. We have changed a lot of things since last year. Eighty-five per cent of the team is new.
"The first step was to arrive with the car in Australia, something that I had doubts about during the pre-season, and we made it. We didn't qualify, but then the next step was to be within the 107 per cent and we have achieved that.
"Then another obstacle we overcame was getting the reliability to finish races. And the final one we just overcame is having a headquarters where we can all work under the same roof to optimise our resources. But it's still an obstacle race and we have only jumped the first ones.
"We have the racing team more or less done. We have to grow a bit in the financial, logistical and administrative areas. We are 75 people and I would like to be able to reach 110. Then we want to bring the design section, at least the chief designer, here [to Madrid]."