Mr Manser was responding to a question on Clark's future in the Whitby Gazette's live webchat on Friday night.
"Yes, Graeme has my total confidence," he said. "We will sit down in the close season to discuss the 2009/10 season."
When asked how the Blues had got themselves into a positiomn where they were battling to stay in the UniBond League's top tier, Mr Manser said too many suspensions resulting from sendings off and bookings were to blame, along with points thrown away against the likes of Ashton United and Kendal.
"We have also had bad luck with injuries.
"I genuinely feel that the quality of the squad is better than 18th," he said.
Commenting on the effect relegation would have on the club, Mr Manser replied: "Disappointment and embarrassment, less travelling, but our aim would be promotion next season.
"The playing budget would remain the same as this season and therefore we would be more competitive."
Mr Manser recently asked Whitby fans to talk to him face to face about any concerns following a number of negative posts on the club's forum.
"I am totally in favour of the online exposure and am quite happy for full and frank discussions, but cannot tolerate abusive comments and derogatory remarks about our players," he said.
"Also, I would like every contributor to use their own name and they should be in the club's weekly draw.
* To see the webchat in full, click here