Sexual Risk Reduction program is one of the frequently implemented programs in college campuses.
is the only correct one.
"implemented" is a past participle, a verbal form, even though here it's used attributively.
Now, let's think about the meaning of:
frequent, implemented program = program that is frequent and is implemented [kind of strange]
frequently implemented program = program that is implemented frequently (in a frequent manner) [makes sense]
Also, search for such combinations at Google Books (not vanilla Google):
"the frequent implemented"
"the frequently implemented"
About 51 results
Thus the 2nd clearly takes it from this point of view too.