The 49ers conducted a purge of the coaching staff soon after their final game, with coach Jim Tomsula, offensive co-ordinator Geep Chryst and most other assistant coaches fired.
Kelly said just running backs coach Tom Rathman, who worked tirelessly to turn Hayne from an NRL backline star last year into an NFL running back, was the only coach assured of returning.
"I think Tom is the best running backs coach in the NFL," Kelly said.
Special teams co-ordinator Thomas McGaughey, who was openly critical of Hayne and replaced him mid-season with Bruce Ellington as punt returner, is still in contention to keep his job.
Kelly said interviews with potential position coaches are continuing, with some scheduled on Wednesday.
Kelly, who transformed the University of Oregon into one of America's top college football teams from 2009 to 2012, became hot property in the NFL with the Buffalo Bills, Cleveland Browns and Philadelphia Eagles pursuing him.
He signed with the Eagles, had immediate success, but the past two years, amid complaints about Kelly's overbearing coaching style and the team missing the playoffs for the second straight year, he was fired one game before the season ended.
If Hayne remains on the roster through to April 4 when the 49ers' 90-man training camp roster convenes in Santa Clara he will have a chance to impress Kelly.
The coach said while he will be viewing tape of players and every game of the past season over coming weeks, it is not until he sees players on the field with his own eyes that he can do a true evaluation.
"Until you see them on the field, you really don't know," he said.
"You'll get an understanding when you look at film, but you need to see guys live.
"You need to see guys running around.
"There's always someone that you kind of saw them on film and you're not really sure about and then you see them in person and you're like, 'Wow, this kid is really special. There's something to him'.
"So I would reserve all judgment on anybody until we get out on the field."
NFL rules ban coaches from talking about football to players before April 4, although Kelly said he has had casual conversations with 49ers players including quarterback Colin Kaepernick and running back Carlos Hyde at the team's Santa Clara headquarters.
Kaepernick, signed to a six-year US$114 million (A$165.34 million) contract, lost his starting job under Tomsula.
Kelly said he has an open mind about Kaepernick and his replacement, Blaine Gabbert.
- AAP
