The Pentagon chief also "encouraged Russia to consider joint [military] initiatives" with Washington and the alliance "that increase transparency [while] enhancing our mutual strategic stability," Defense Department spokesman George Little said Wednesday.
The Obama administration plans to field a massive network of land and sea-based ballistic missile interceptors in eastern Europe, to defend against Iranian long-range missile threats by 2020.
American and NATO officials plan to break ground on the first missile defense radar site in Romania next week.
But Moscow has been adamantly opposed to the shield, arguing the weapons designed to counter the Iranian threat could easily be used to take out Russian-operated missile systems stationed in the region.
That said, Moscow has demanded that NATO sign an agreement guaranteeing that none of the weapons included in the missile shield would be used to neutralize the country's own missile defense system.
NATO leaders declined to sign any such agreement and refused to hand over joint control of the shield to Russia. Since then, Washington and Moscow have been at loggerheads over the issue.
Since then, U.S.-Russian relations have broken down even further, in the wake of Moscow's decision to grant asylum to former NSA contractor Edward Snowden and Russia's support of Syrian President Bashar Assad's regime.
But the Pentagon and Obama White House are looking to repair those frayed international ties with Russia.
In addition to Hagel's guarantees on the U.S. missile defense shield, both defense leaders -- for the first time -- agreed to hold regular one-on-one teleconferences to discuss regional security issues.
"This new security cooperation channel can help lay a foundation for progress in what's an important military-to- military relationship," Hagel said during a Wednesday press conference in Brussels.
Pentagon and Russian military officials are drafting possible agendas and coordinating when the first of these teleconferences will take place, according to Hagel.
"The point being we could use at least the initial teleconferences to ... have a very open, transparent and frank discussion about not just where we agree, but where we disagree, how we might be able to accommodate each other in some of these areas," the Pentagon chief said.
In light of the turbulent relationship between the two nations, the teleconferences will help Washington and Moscow to head off potential security threats "rather than waiting for a crisis and [being] forced together to communicate because ... something's blowing up in the world."
Hagel admitted that despite both countries' best efforts, "we're going to continue to have differences" on regional security and defense issues.
"I think it's always smarter and better for everyone if ... [we can] deal directly with our differences and find common interests and enhance ways where we can cooperate," he said.