In the letter written by her from Bhopal, Bharti said she is saddened by media reports which have "needlessly made me a part of the controversy".
She said this has caused an embarrasment to the party President.
"I am with you on all decisions that you take. Whatever decision you take in Goa has my prior support. I can never keep a contradictory view. Other than our political relations, you and I have a brother-sister relationship for the last 30 years. I am always with you," Bharti said.
There were reports that Bharti, Yashwant Sinha, Jaswant Singh, Shatrughan Sinha and B C Khanduri have skipped the conclave in solidarity with Advani.
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Bharti's letter appears to be aimed at distancing her from the controversy.
"I apologise to you and the entire National Executive for any embarrasment caused due to me," she said in her letter.
She changed her plans and stayed in Bhopal instead of going to Delhi to join Singh and fly with him.