The 68 year old German was also joined by assistant Piet Hamburg after an apparent dispute over match bonuses for Sparrow Hawks players.
Togo team official Messan Attolou announced Pfister would be replaced by former assistant Kodjovi Mawuena until further notice.
"Is Kodjovi Mawuena going to be the new coach on a permanent basis? We will see. Otto Pfister has not given us a definitive 'no' yet," he told AFP.
FIFA have also confirmed that coaches are not governed by the same strict rules as players and could be replaced during the tournament.
The former Saudi Arabian coach was yet to guide Togo through a competitive match after he had taken over from Nigerian Stephen Keshi who was sacked after Togo were eliminated in the first round of this year’s African Cup of Nations.
Togo face South Korea in their first match of Group G on June 13 in Frankfurt.