"Is Assad being benefited, helped by what we're doing, other countries against ISIL? He's indirectly benefiting," Hagel said in an interview with CBS News.
The Pentagon chief said the military action was a long-term campaign focused on destroying the terrorist organization not overthrowing the Syrian government.
“We've never seen an organization like ISIL that is so well-organized, so well-trained, so well-funded, so strategic, so brutal, so completely ruthless," Hagel said, adding that the sophistication of the group’s social media program has made it an “incredibly powerful new threat.”
US President Barack Obama first ordered airstrikes against ISIL targets in September, using Syrian airspace. The air campaign is an extension of air raids in Iraq conducted since August.
The US president has also tasked the CIA and the Pentagon to arm and train “moderate” militants into a proxy ground army against both ISIL and the Syrian government.
The latest setbacks to that strategy came earlier this month when two key US-backed militant groups were routed by Jabhat al-Nusra, al-Qaeda’s primary affiliate in Syria.
Obama has reportedly asked his national security team to review the strategy toward Syria after concluding that ISIL may not be defeated with President Assad in power.
The United States and its regional allies -- especially Qatar, Saudi Arabia and Turkey -- have been supporting the militants operating inside Syria since the beginning of the crisis in 2011.