The Republic of Ireland international was forced off during Everton's 2-0 UEFA Europa League win at Wolfsburg on Thursday, lasting just 31 minutes in Germany.
It was not the first time this season that the 24-year-old has had problems with his hamstring, with the midfielder missing Ireland's recent matches against Germany and Scotland, incurring the wrath of Martin O'Neill's assistant Roy Keane.
Martinez revealed that the injury itself is by no means serious, but he is determined not to rush McCarthy back as the club looks to finally get to the bottom of the issue.
"It's a soft tissue problem, which is not down to fatigue," the Spaniard said. "It's the hamstring he's had struggles with. We're going to assess him.
"It is a problem we need to look at because he has had it before.
"His body is getting used to the demands of playing European football and international football. We need to make sure we find the right balance. We're going to help him in that respect.
"James wants to be play. He does for any competition and I love that from him. But it reaches a point where we have to give him the right rest.
"What I'm focusing on is getting deep into the bottom of the problem and slowly allowing him to cope with the demands his role represents."
McCarthy looks set to miss Sunday's trip to Tottenham as a result of his latest injury, but Martinez may be able to welcome back four key players.
"There are two different groups; one with four players who we need to assess for the weekend and who have an opportunity to be part of the squad," he explained.
"That's Gareth Barry, Steven Naismith, Leighton Baines and Steven Pienaar.
"Darron Gibson, Bryan Oviedo, John Stones and Antolin Alcaraz are progressing well but they need a little bit more time."
