The new act says chaplains can only preside over gay and lesbian weddings if state and local laws allow, CNN reported.
"A military chaplain may participate in or officiate any private ceremony, whether on or off a military installation, provided that the ceremony is not prohibited by applicable state and local law," a memo from Undersecretary of Defense Clifford Stanley, released Friday, says.
The memo goes on to say chaplains are not required to officiate a marriage if it conflicts with their religious beliefs.
"Further a chaplain is not required to participate in or officiate a private ceremony if doing so would be in variance with the tenets of his or her religion."
In May, the Navy first permitted same-sex weddings on military bases, then later prohibited the change.
Stanley's memo stopped short of fully supporting gay marriages, ending with "a military chaplain's participation in a private ceremony does not constitute an endorsement of the ceremony" by the Department of Defense.