Jones (Betty Francis) announced her pregnancy in April of last year, forcing the AMC drama to reschedule shooting.
"We had to move things around because of January's pregnancy," Weiner confirmed to The Huffington Post. "She was out for a chunk of the season, and she should be allowed to be."
Asked how large a role Jones would play in the new season, he added: "Yeah, she's not in it that much, but you know, that's biological reality."
Jones recently admitted that she often finds herself defending Betty, insisting that the character's actions are "justified".
Her co-star John Slattery also praised the actress after she was accused of being unapproachable by a former child actor on the show.
The new season of Mad Men premieres on Sunday (March 25) at 9/8c on AMC, and will air in the UK two days later on Sky Atlantic.
> Mad Men: The 10 Greatest Moments from Four Seasons
> Mad Men Jon Hamm interview: It won't end with Don Draper in the 1990s
Watch a trailer for the new season of Mad Men below: