In a statement, Keys said she asked for "corrective actions" as soon as she came to know about the advertisements.
The company has withdrawn their sponsorship and the billboard posters have also been removed.
"I apologize for any misleading advertising initially associated with the show," BBC quoted Keys, as saying in a statement.
"I''m an unyielding advocate for the well-being and health of children around the world and do not condone or endorse smoking.
"I look forward to bringing my music and message to my wonderful fans in Jakarta," she added.
Keys was condemned by anti-smoking campaigners, who claimed that the deal would encourage young fans to take up smoking.
The campaigning organisation Tobacco Free Kids said the branding was "inconsistent with (Keys'') advocacy for children's health through her involvement in Keep A Child Alive, a campaign to address the HIV/AIDS epidemic in poor countries".