McCarthy, 20, sat out the Republic of Ireland's Carling Nations Cup victory against Wales on Tuesday as he only recently recovered from an ankle injury and Martinez did not want him to be risked. However, his absence led to widespread speculation the Glasgow-born player - who qualifies for Ireland through his grandfather - could yet switch sides ahead of next month's Euro 2012 qualifiers.
Martinez insists the injury was genuine and that he does not have an issue with Republic manager Giovanni Trapattoni regarding McCarthy, who was withdrawn after he scored twice in the 4-3 victory against Blackburn.
"James has had four games in 12 days. He could not finish the 90 minutes in the last game," he said.
"We sent a report to the Republic medical staff and I spoke with Mr Trapattoni. Everything is quite clear. He could not be involved.
"He needed to have some treatment and regenerate and just be ready for Saturday. They understood that and know exactly what he has been through. James needs to be 100% to perform and club level and international level."