Industry claims the directive could have "devastating" economic effects on some countries in Europe and beyond.
Speaking at an anti-tobacco conference in New Delhi, Chan said a "massive army" of over one hundred lobbyists had been deployed to block the bill's passage, backing a report published in The Guardian newspaper.
"The most recent example concerns efforts on the part of Philip Morris to sabotage the vote on a strong European directive on tobacco," Chan told the conference, attended by delegates from over 55 countries according to the AFP news agency.
She said the lobbyists were seeking to delay passage of the rules until the rotating European Council presidency moves to Greece from Lithuania in January.
This would force the complex process for passing the measure into law to start again. While Lithuania favours tobacco controls, Greece, with one of the largest percentages of smokers in the world, opposes strong regulation.
The vote in Parliament was planned for 10 September, but last week the leaders of the main centre-right political groups in Parliament – the European People's Party (EPP), the Alliance of Liberals and Democrats for Europe (ALDE) and the European Conservatives and Reformist Group (ECR) – colluded to postpone the vote until 8 October.
New distribution centre in Greece
The proposed update of the tobacco directive includes mandatory pictorial health warnings covering 75% of a cigarette package, front and back. MEPs will also consider regulating the increasingly popular e-cigarettes and banning slim cigarettes aimed at young women.
Chan noted that Philip Morris was opening a European distribution centre in Greece, whose government has hailed the investment as "important and symbolic".
"Here industry is counting on the historical pattern where economic and commercial interests trump public health concerns," she told the conference, according to AFP.
Last week the British newspaperThe Guardian published leaked documents which it claimed showed that Philip Morris had spent large sums to get the EU vote postponed or derailed.
Tobacco lobbyists in Brussels say that the EU's proposal to regulate cigarette ingredients, "drafted by just seven members of the Parliament", could threaten the jobs of more than 600,000 tobacco farmers in Europe, Africa and the US.
One tobacco industry representative told EurActiv that the amendment creates a de-facto ban on adding any ingredients to tobacco products, beyond tobacco leaf itself.
"While on the surface the lawmakers' proposal seems reasonable, this could be extremely detrimental to farmers growing Burley variants of tobacco leaf, which require the addition of ingredients like sugar in the manufacturing process to compensate for the elements that are lost during curing," he said.
By indirectly targeting Burley tobacco farmers, this could be "devastating" for countries such as Poland, Italy, France, Spain and Bulgaria where 9,000 burley farmers sell 90% of their product to the EU, the industry representative said.
Farmers in Malawi, Mozambique and the state of Kentucky in the US would also be hit by the directive, he added.