The batsman was not selected for this month's limited-overs series with South Africa and the World Twenty20 competition in Sri Lanka next month following his well-documented problems with Andrew Strauss and Andy Flower.
Former England captain Stewart was not shocked by the decision and believes that there are still plenty of discussions ahead before Pietersen's path to return to international cricket is clear.
Stewart told BBC Sport: "There are still issues to be sorted out and England captain Andrew Strauss said after the game that they need to discuss them before any decisions are made.
"I'm sure it was no surprise to Pietersen himself that he wasn't picked - and he will know that until those problems are resolved he won't be selected."
Ravi Bopara has been included in both squads after a break from cricket due to personal reasons.