The book "Inferno," which is being sold in the Philippines, describes a visitor to the city who is taken aback by poverty, crime and prostitution.
The chairman of metropolitan Manila, Francis Tolentino, wrote an open letter to Brown on Thursday, saying that while "Inferno" is fiction, "we are greatly disappointed by your inaccurate portrayal of our beloved metropolis."
Tolentino objected to the "gates of hell" description, and to Manila being defined by what he calls terrible descriptions of poverty and pollution.
He said that the novel fails to acknowledge Filipinos' good character and compassion.
"Truly, our place is an entry to heaven," Tolentino said. "We hope that this letter enlightens you and may it guide you the next time you cite Manila in any of your works."
Brown's publisher, Doubleday, declined comment when contacted by The Associated Press.
"Inferno" is already a best-seller a little over a week since its debut. The story drawn partly from Dante's epic again features Harvard symbologist Robert Langdon, the protagonist for Brown's blockbuster "The Da Vinci Code" and its follow-up "The Lost Symbol."
In the book, Langdon's companion depicts Manila as a city of "six-hour traffic jams, suffocating pollution, horrifying sex trade."
"I've run through the gates of hell," she said.
It's not the first time that authorities have been angered by an unflattering description of the sprawling city of some 12 million people, where urban shanties and the homeless exist side by side with glitzy shopping malls and walled residential compounds.
In 1999, then-President Joseph Estrada banned Hollywood actress Claire Danes, who shot the movie "Brokedown Palace" in Manila, from entering the country after she said in an interview that the city was smelly, weird and full of rats.
Estrada was elected mayor of Manila in last week's elections on a promise to reverse the city's decay.