Namibia were beaten 1-0 at home by Malawi in Windhoek on Saturday, their second defeat in three Group F matches.
"I think the time has come to part ways with the association because I failed in my mission to qualify the team for both the Africa Cup of Nations and the World Cup," Kaanjuka told reporters.
He effectively wrote off Namibia's chances with three matches still to play even though they are only two points behind co-leaders Nigeria and Malawi.
Kaanjuka had been in the job for the last 18 months and won four of 15 matches in charge.
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