The U.S. military will give flu shots to troops in Iraq and other key areas overseas and to high-risk family dependents, but thousands of others will go unprotected this year, the Pentagon said on Thursday.

“We will be working with roughly 60 percent of our originally projected vaccine supply,” Assistant Defense Secretary for Health Affairs William Winkenwerder told reporters.

He called the situation “very manageable.”

U.S. health officials have been stung by political attacks after losing 40 percent of the flu shot supply. The United States is far short of the 100 million doses that had been planned after Chiron Corp lost the license for a British vaccine plant on Oct. 5.

The Defense Department had expected to receive about 3.6 million to 3.7 million doses, but instead will be working with roughly 2.1 million doses, Winkenwerder said.

Pentagon officials said U.S. troops in areas such as Iraq, Afghanistan and South Korea will get shots. But they conceded that large numbers of the 1.4 million active-duty troops and thousands of family members who normally receive shots will not get them this year.

Winkenwerder said priorities for dependents and others similar to those in the public health system were being set up.

He said children aged 6 months to 2 years as well as military dependents 65 years old or older would get priority immunizations along with pregnant women and others in high-risk categories.

“Our plan is to ensure that all of our operationally deployed service members and all of our high-risk beneficiaries will be vaccinated this flu season and will be vaccinated on time,” he said.