"It [vetting] is of course an issue we must pass through, and ultimately successfully completing the training, then successfully protecting that force, so that it does have operational capabilities," Allen said on Monday.
"It's clearly part of our plan. Not only will we train them, but we will equip them with the latest weapons systems, but we will also protect them when the time comes," Allen said.
When asked how they are going to deploy 5,000 vetted Syrian rebels inside Syria without any ground or air cover, with no safe corridors, and with no fly zones, Allen underlined that all these things were under consideration.
"We are pleased with the numbers that have said that they want to be part of this," Allen said.
The United States and its allies plan to train and equip some 5,000 Syrian opposition fighters as part of their efforts to battle the ISIL.
On February 19, US Department of Defense Press Secretary John Kirby announced that the United States has been screening about 1,200 moderate Syrian rebels as candidates for a US training program.
The program that focuses on basic military equipment and skills will start once the training sights are ready, according to the Pentagon.
In January, the Defense Department announced that an advance team of about 100 US troops was deployed in the Middle East to survey and prepare training locations.
The US-led coalition against the Islamic State began carrying out airstrikes in Iraq in August, expanding the air campaign to Syria in September, though without Syrian government approval.
The ISIL, also known as the Islamic State of Iraq and Syria (ISIS) and the Islamic State of Iraq and the Levant (ISIL), is a Sunni military group that has taken over large portions of Syria and Iraq and declared a caliphate.