Wagner is under increasing pressure after Cologne collected just nine points from their opening nine league matches, leaving the club 15th in the table. However, Kessler believes the team needs stability rather than another immediate change in the dugout.
Speaking on the Geisstalk programme, the 40-year-old stressed the importance of giving a project time to develop.
"I think there are many examples in German football where a certain consistency and calmness, which is difficult for us to maintain, have led to things being built. I see us, even if one or two fans would certainly disagree with me, as being fundamentally on a good path," Kessler said.
The sporting director acknowledged that results must improve if the club is to maintain confidence in the current direction.
"We obviously need points along this path. Through points, you gain confidence, and that also gives you a little bit of calm," he explained.
Cologne have struggled for consistency, with their position in the bottom half of the table placing Wagner under scrutiny. Their most recent league fixture before the international break ended in a 2-1 home defeat against Bayer Leverkusen, extending their winless run to four matches.
Kessler nevertheless made clear that he is not currently considering a managerial change. He also pointed to the importance of being able to act if the club's progress stalls completely.
"There are situations, as I experienced last season, when I get the impression that continuity isn't helping. Then, at 1. FC Köln, we are obviously always capable of taking action," he said.
The sporting director insisted that the club would not hesitate to intervene if he became convinced that the team was moving in the wrong direction.
"Nobody needs to worry that we wouldn't be in a position to act against things if I had the conviction that we weren't on the right path."
However, Kessler was unwilling to offer Wagner an unconditional guarantee.
"In a world like professional football, where we operate at the highest level of professional sport, nobody can give any kind of job guarantees," he added.
Cologne's immediate challenge is to turn their performances into points, with a difficult trip to Bayern Munich scheduled for November 20 before a home fixture against Elversberg.
For Wagner, those matches could prove important in determining whether the club's faith in continuity is rewarded.