More than 100 people have contacted the corporation to raise concerns over the plot, which saw Michael (Steve John Shepherd) con Jean out of a substantial sum of money before launching an elaborate plan to discredit her.
Jean, who suffers from bipolar disorder, was doubted by a number of Albert Square's residents as the story played out. However, Michael finally confessed his guilt in last Friday's (June 22) episode.
It is thought that some viewers were unhappy over the cruel treatment Jean received in the storyline. A statement released on the BBC's website has confirmed that others felt "the depiction of bipolar, as portrayed through Jean Slater, is unrealistic".
In response, the corporation said: "It is important to note that Jean Slater is not intended to be representative of everybody with bipolar disorder. We treat all of our characters as individuals, with their own sets of behaviours and opinions, and there's no suggestion that all of Jean's characteristics are linked to her condition.
"We work closely with a number of experts in the mental health field to ensure that we are as accurate as possible when it comes to Jean's bipolar, her medication, the impact it has on her and those around her, and attitudes and prejudices towards her."
The statement added: "Michael is a well-established villain, intent on destroying others for his own twisted motives, and the current storyline is completely in keeping with his character.
"The audience were aware from the start that it was Jean who was telling the truth even when other characters doubted her. In Friday's episode Alfie, Kat and Janine learned the truth, and Jean was completely exonerated."
In a separate statement, a BBC spokesperson confirmed the total number of complaints.
The representative told The Daily Telegraph: "We have received a total of 107 complaints from over 16 episodes. As every EastEnders viewer will know, this storyline has been running for over a month, with the climax reaching over eight million viewers.
"The storyline was never about Jean's bipolar disorder but about how Michael has manipulated her."
Actress Gillian Wright has played the role of Jean on and off since 2004. Her portrayal of Jean's bipolar disorder has previously received acclaim from the mental health charity Mind.