"It is horrific to think that an industry known for its dirty tricks and dirty laundry could be allowed to trump what is clearly in the public's best interests," Chan said at a WHO meeting in the Philippine capital on Monday.
Chan cited legal actions by the tobacco industry against anti-smoking measures in Australia and Uruguay, saying these were "scare tactics" intended to frighten other countries from following suit.
"It is hard for any country to bear the financial burden of this kind of litigation, but most especially so for small countries," she said.
"Big tobacco can afford to hire the best lawyers and PR firms that money can buy. Big money can speak louder than any moral, ethical or public health argument and can trample even the most damning scientific evidence".
Chan called on the countries at the forum of Western Pacific nations to fight back.
"I urge all these countries to stand firm together, do not bow to pressure... we must never allow the tobacco industry to get the upper hand," she said.
Chan pointed to successful efforts in the Philippines to increase taxes on tobacco products, saying that the WHO was "gearing up" to support other countries that took such measures.
Chan did not specify how the WHO would help countries in their efforts to combat the tobacco industry.
But the WHO has for many years called for bans on cigarette advertising and promotion, as well as restrictions on smoking in public places and higher taxes.
In Australia, Prime Minister Julia Gillard's government is aiming to introduce world-first legislation that would force all cigarettes to be sold in plain packaging from January 1 next year.
However Philip Morris has launched legal action, claiming Australia's plans violate international trade obligations and warning it expects billions of dollars in compensation if plain packaging goes ahead.
Australian Department of Health Secretary Jane Halton told the WHO forum in Manila that her government was determined to push through with its plan, despite the "subversive tactics" of tobacco companies.
"We stand ready to repel the assault of big tobacco but we acknowledge it will be a big fight," Halton told the WHO delegates.
WHO documents released at the forum said that 3,000 people die each day from tobacco use in the Western Pacific region.This covers an area with a population of 1.6 billion people, including China, Australia, Japan, South Korea, Mongolia, the Philippines, Vietnam, Cambodia, Malaysia, Singapore, Brunei and many South Pacific island nations.