Martinez revealed that Barkley may be missing for a "while" because the injury is more serious than first thought.
"Ross had a knock in his toe against Queens Park Rangers and we all felt that it would settle and he'd be able to play today," the Spaniard said on the club website.
"As it turned out, I think it's a bit more serious than we expected and it could be a fracture in his metatarsal and we need to assess it in the next few days."
"We're going to assess it to see if there was displacement or not, it's a very similar incident to the one Leighton Baines had," Martinez told the BBC, referring to his England left back who returned to the team at Christmas after a month out.
"We're going away to do some warm weather training and that's going to help Ross heal his bone and hopefully he'll get back quicker than we expect," added Martinez whose squad will go to Tenerife before next week's visit to West Bromwich Albion.
"It is a blow but in the same way, at such a young age, we're going to use this as a perfect rest for him to come back and be as strong and as sharp as he can be in the second half of the season."
Barkley has put in a string of impressive displays this term as Everton, who are in fourth place five points behind leaders Chelsea, push for a spot in next season's Champions League.
His performances have also earned him three England caps and he is in the frame for a place in Roy Hodgson's World Cup squad.