Speaking to the BBC, regional director Dr Hans Kluge warned that 500,000 more deaths could be recorded by March unless urgent action is taken.
Dr Kluge said an increase in mask wearing could immediately help.
The warning comes as several nations report record-high infection rates and introduce full and partial lockdowns.
Dr Kluge said factors like the winter season, insufficient vaccine coverage and the regional dominance of the more transmissible Delta variant were behind the spread.
He called for increased vaccine uptake and the implementation of basic public health measures and new medical treatments to help fight the rise.
Covid-19 has become once again the number one cause of mortality in our region,” he told the BBC, adding “we know what needs to be done” in order to fight the virus.
Dr Kluge said mandatory vaccination measures should be seen as a “last resort” but that it would be “very timely” to have a “legal and societal debate” about the issue.
“Before that, there are other means like the Covid pass,” he said, adding that this is “not a restriction of liberty, rather it is a tool to keep our individual freedom.”
Austria on Friday became the first European country to announce that Covid-19 vaccination would become a legal requirement. The new rules are set to come into force in February, as details of how the measure will be enforced are still being discussed.
Austrian Chancellor Alexander Schallenberg said it was a difficult decision to take in a free society, but that the jabs were “the only exit ticket we have to break this vicious circle”.
“It’s a problem for the whole society because even those that are vaccinated, if they don’t have access to an intensive care unit because they’re blocked by those who are not vaccinated and got sick, so then they are affected as well,” Mr Schallenberg told the BBC.
On Saturday, tens of thousands of people protested against the new measures in the capital Vienna. Many waved signs with slogans such as “no to vaccination” and “enough is enough”.
Many other European countries are also imposing new measures as cases rise.