Roberto Azevedo said diplomats from the WTO's 159 members tried hard but "cannot cross the finish line here in Geneva" ahead of a summit where ministers were to have signed the deal in Bali, Indonesia next week.
The diplomats became deadlocked over the details in the past few days and there remains so much disagreement that several more weeks of negotiations could close the gaps and it will not be possible to negotiate the final details in Bali, he said.
In recent years, trade talks have progressed more speedily when they involved only two sides. The European Union, for example, has clinched free trade deals with South Korea and later Canada. It is in separate talks with the US and Japan as well.
But the failure to reach a global deal would "have grave consequences for the multilateral trade system" and hurt the WTO's credibility, Azevedo said, because the organisation will only be viewed as a trade court and no longer as a forum for governments to negotiate trade agreements.