Pepe trained by himself on Tuesday in his attempts to recover in time for Portugal's Euro 2016 semi-final against Wales.
The Real Madrid defender remains a doubt because of the thigh injury that meant he missed training on Monday. Portugal's staff continue to monitor his condition.
Should he not be passed fit for Wednesday's fixture at the Stade de Lyon, 38-year-old Ricardo Carvalho is expected to replace him.
Pepe, 33, remains a key figure in coach Fernando Santos' team and plays alongside Wales' Gareth Bale at club level.
His potential absence comes at a time when Wales will be without the suspended Aaron Ramsey and Ben Davies.