Defense Secretary Lloyd Austin(C), Chairman of the Joint Chiefs of Staff Gen. Mark Milley(L), and Commander of US Central and Command Gen. Kenneth McKenzie(R) testify before the Senate Armed Services Committee on Afghanistan, in the Dirksen Senate Office Building on Capitol Hill in Washington, DC on September 28, 2021. (Photo by MANDEL NGAN / AFP) (Photo by MANDEL NGAN/AFP via Getty Images)
CNN  — 

Top military officials warned Tuesday that the war in Afghanistan and the war on terror are not over, even if the US military no longer maintains boots on the ground after 20 years of a consistent military presence in the country.

Secretary of Defense Lloyd Austin, Chairman of the Joint Chiefs of Staff Gen. Mark Milley and head of US Central Command Gen. Frank McKenzie faced a grilling from lawmakers on the Senate Armed Services Committee who wanted to know how the US military presence ended with images of Afghans clinging onto US military planes, how a drone strike killed 10 Afghan civilians and how Americans citizens and Afghans who helped the US during America’s longest war got left behind in the evacuation effort.

Here are five takeaways from the Senate hearing:

The war in Afghanistan and the war on terror are not over

Both Milley and McKenzie, the top US military commander in the Middle East, acknowledged that while no US troops remain on the ground in Afghanistan, neither the war on terror nor the war in Afghanistan are over.

When asked by Sen. Thom Tillis, a Republican from North Carolina, if either military effort was finished, both generals said no.

“The war on terror is not over, and the war in Afghanistan is not over either,” McKenzie said.

Tillis also asked the generals if withdrawing the US military from Afghanistan has made it easier or more difficult to protect the US from potential threats. Both Milley and McKenzie said the withdrawal has made protecting the US “more challenging.”

Military leaders advocated for keeping troops in Afghanistan

Both Milley and McKenzie said they supported keeping 2,500 US troops in Afghanistan. Milley said he held that opinion in the fall of 2020 and his position “remained consistent throughout,” that the US should keep “a steady state of 2,500 and it could bounce up to 3,500 … in order to move toward a negotiated solution.”

While both McKenzie and Milley would not comment on conversations they had with President Joe Biden after he took office in January 2021, they asserted that keeping 2,500 troops in Afghanistan was their position.

Austin told the committee that “input was received” and “considered by the President” before Biden made his decision to withdraw US troops from Afghanistan in April.

When Republican Sen. Tom Cotton of Arkansas asked Milley why he didn’t resign after Biden decided to pull troops from the country, Milley said his job is to provide “advice” to the President, but “the President doesn’t have to agree with that advice.”

“This country doesn’t want generals, figuring out what orders we are going to accept and do or not,” Milley said. “That’s not our job. The principle of civilian control of the military is absolute, it’s critical, to this republic.”

Keeping al Qaeda and ISIS in check will now be harder

McKenzie believes it will be harder for US Central Command to prevent terrorist organizations from gaining strength in the region now that the US is no longer in Afghanistan.

“I have … the ability to look into Afghanistan” from US Central Command headquarters, but it is “limited,” McKenzie said.

McKenzie also said he was not confident in the US’ ability to prevent ISIS and al Qaeda from using Afghanistan as a launchpad for terrorist activity in the future.

“I think we’re, you know, we’re still seeing how al Qaeda and ISIS are configuring themselves against the Taliban, we’re still seeing what the Taliban is going to do,” McKenzie said. “I would not say I’m confident that that’s going to be on the ground yet, we could get to that point, but I do not yet have that level of confidence.”

Doha agreement ‘lowered morale’ of Afghan forces

Milley, Austin and McKenzie all said the Doha agreement, brokered during the Trump administration, lowered morale of the Afghan National Defense and Security forces.

McKenzie called the agreement “the primary accelerant to lowering morale and general efficiency of the Afghan military.”

Austin said the agreement had a “significant impact on the morale of the troops.”

Austin said he believed the swift collapse of Afghan forces was driven by series of factors, including a lack of morale after the Doha agreement, along with weak leadership within the forces, and corruption in the Afghan government.

Milley: US credibility has been damaged

Milley said he believes US credibility has been damaged after the US withdrawal, which triggered the withdrawal of all NATO allied troops stationed in Afghanistan alongside Americans.

“I think that our credibility with allies and partners around the world, and with adversaries, is being intensely reviewed by them to see which way this is going to go. And I think that ‘damage’ is one word that could be used, yes,” Milley told Sen. Roger Wicker, a Republican from Mississippi.

The three top military leaders will appear before the House Armed Services Committee on Wednesday to face questions from House Democrats and Republicans about the US withdrawal from Afghanistan.

CNN’s Michael Conte, Jennifer Hansler and Oren Liebermann contributed to this report.