Phil (Steve McFadden) and Rainie (Tanya Franks) were seen using crack cocaine in Monday night's episode, which The Sun reports prompted over 200 complaints.
In a statement the BBC said: "EastEnders has a history of tackling social issues and this drugs storyline follows that tradition.
"We acknowledge that some viewers may consider this storyline challenging, however EastEnders in no way - and at no point - glamorises or condones the use of drugs, and furthermore we took great care to avoid any demonstration on how to prepare or take drugs."
It continued: "We feel that Phil's decline will highlight the destructive nature of drugs, and rather than encourage drug use, will act as a deterrent."
The statement goes on to say that care was taken to warn viewer's about the episode's content through "programme publicity and billings". The corporation's Action Line was also highlighted for anyone affected by the issues.
"We worked closely with drug and alcohol charities, including Addaction and DrugScope, throughout the editorial process to ensure that we handled the storyline accurately and sensitively," the statement added.
Tanya Franks recently told DS that the show had been "brave" to highlight the issue "within the restrictions of the timeslot".
Last month the BBC soap was forced to defend itself following complaints about the treatment of the Qu'ran and the Lucas Johnson storyline.