Samba, who has been linked with Tottenham, QPR and Paris Saint-Germain, missed Saturday's win over Fulham after calling in sick the previous day.
His absence aroused suspicion, however, as it came in the wake of an interview he did with L'Equipe in which he was quoted as saying, "It is time for a change".
However, Kean is determined to hang on to Samba, who signed a new five-year contract with the club almost a year ago.
"He's not for sale, it's as simple as that," he told the Lancashire Telegraph.
"He'll be back in again and hopefully ready for Everton."
The club are not commenting on a letter by former Rovers directors to owners Venky's which was made public over the weekend.
Ex-chairman John Williams, Tom Finn, the then managing director, and Martin Goodman, formerly the finance director, wrote to co-owner Anuradha Desai last January expressing their concerns about the way the club was being run.
All three have since left Ewood Park and although Paul Hunt was hired as deputy chief executive and Karen Silk replaced Goodman concerns remain among fans, many of whom have been protesting against the India-based owners for the last few months.
In the letter the trio expressed their worries that the board on which they sat was being marginalised in the decision-making processes at Ewood Park and that Kean, who at that time had been in the job less than a month, needed greater support.
It is a situation which many feel still needs addressing with Kean still looking for assistant coach to replace Paul Clement, who was in the job for less than three months before moving to Paris St Germain to be reunited with former Chelsea manager Carlo Ancelotti.
Eric Black, formerly Steve Bruce's assistant at Sunderland, and ex-Blackburn midfielder Billy McKinlay, currently working as a youth coach at Fulham, have been linked with the job.