The Magpies denied in a statement Monday it had prevented Martins from joining the Nigeria squad.
Newcastle manager Glenn Roeder said last month he would ask for Martins to sit out the game because he is the club's only fit striker. Michael Owen and Shola Ameobi are out for the season
"A young kid of 19, playing five consecutive matches, running 12 kilometres a game, of course the boy is a little tired and he felt a little pain," Mourinho said.
"We have to scan it, but experience says he has a little muscular problem and for the next 15 days, he is out of competition."
Mikel will miss Saturday's game with Middlesbrough, the FA Cup fifth round tie with Blackpool or Norwich, and the first leg of the Champions League clash with FC Porto.
Due to the injury list at Stamford Bridge forcing Michael Essien to play in defence, Mikel has capitalised on his chance in the first-team.
He has made an appearance in all of the Premiership champions' games in 2007 and scored in the 3-0 win over Nottingham Forest in the FA Cup fourth round tie last month.