The 10-times Grammy-winning artist, who has sold 20 million albums worldwide has a gig in Jakarta, Indonesia, on Tuesday.
Campaigning organisation Tobacco Free Kids says adverts for the concert act as billboards for tobacco firm Philip Morris International and its Indonesian subsidiary, Sampoerna.
Ms Keys accepted the charity's accusation and insisted action had been taken
to remove the offending adverts.
She said: "When I was informed that my July 31 As I Am concert in Jakarta, Indonesia was partly sponsored by a tobacco company, I immediately asked for an investigation and that corrective actions be taken.
"As a result, the tobacco company has respectfully withdrawn their sponsorship and all billboards, signage and other forms of advertising will be immediately removed."
Giant posters in the Indonesian capital advertised the gig as a "Mild Live Production" - a reference to a cigarette brand produced by Sampoerna. They also carried a large health warning that states: "Smoking can cause cancer, heart attacks, impotence and harm pregnancy and foetal development. "
In the US, Philip Morris USA and other major tobacco companies are prohibited from engaging in brand name sponsorships of concerts under a 1998 legal settlement with the states," said a statement from the charity.
"However, in developing countries, tobacco companies continue to sponsor concerts by famous musicians, which health advocates have condemned as a means to market cigarettes to children and to circumvent restrictions on more traditional tobacco advertising.
The charity 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".
Ms Keys responded that she did not "condone or endorse" smoking and apologised for "any misleading advertising initially associated with the show".
The charity said that about 35% of the Indonesian population smokes, and tobacco use kills more than 200,000 Indonesians each year. An estimated 78 percent of Indonesian smokers started before the age of 19, it added