"I remind the [Defense] Department of its obligation to keep Congress advised as it relates to plans to modify rights and benefits of our armed forces," Inhofe wrote in the letter sent to the Pentagon on Thursday.
In July, Hagel ordered the Pentagon to begin offering full benefits to same-sex military couples after the Defense of Marriage Act (DOMA) was struck down by the Supreme Court.
In February, the Pentagon extended more than 40 new benefits to spouses of gay and lesbian service members, but many important benefits were not extended due to federal restrictions under DOMA.
As part of the department's decision in July, Pentagon officials included a clause allowing gay and lesbian service members a maximum of 10 days of uncharged leave.
The move, according to department officials, was to allow service members stationed in states that do no recognize same-sex marriages time to travel with their partners to get married in states that recognize those unions.
However, heterosexual service members have not been granted that same benefit if they want to marry their husbands or wives.
Aside from questions over the Pentagon's legal authority to grant uncharged leave to same-sex couples and not others, Inhofe chastised Hagel for not notifying Congress of the extension of that particular benefit.
"It is necessary that the Senate must first consider the implication of such a policy before the Department of Defense implements a modification" to Pentagon policies concerning charged and uncharged leave, according to Inhofe.
But the Oklahoma Republican made clear despite his concerns over the uncharged leave clause, he firmly supports the Pentagon's decision to recognize same-sex couples' eligibility for full benefits in the military.
"However, this change in [leave] policy will create disparate treatment between same-sex and opposite-sex couples in our armed forces contrary to the department’s stated policy," he wrote.
Shortly after Hagel's announcement, Inhofe said he was not planning to oppose the Pentagon plan.
“I pick fights that I can win, and right now, my fight is on overregulation,” Inhofe told The Hill at the time.