“Palmgren tendered his resignation due to serious threats directed toward him and his family,” a national football association statement said.
The Swede’s resignation comes just 48 hours before the ‘Brave Warriors’ host Group F leaders Nigeria in a must-win 2014 World Cup qualifier.
Namibia have to collect maximum points at Sam Nujoma Stadium Wednesday to keep alive slim hopes of making the 10-nation final elimination round.
Former Sierra Leone and Rwanda coach Palmgren, 50, took over only last month and his first competitive outing was a 0-0 World Cup qualifying draw in Malawi.
National team assistant coaches Ricardo Mannetti and Ronnie Kanalelo have been put in charge for the Nigeria game.
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