"Otto Pfister left the hotel with his co-trainer Piet Hamberg at 2220 (local time)," team doctor Joachim Schubert was quoted as saying on the website of the respected German magazine Kicker early on Saturday.
"It is too bad he's left because it worked well, Togo and Otto Pfister. But the situation was no longer sustainable for the coach," he said of the 68-year-old German.
Rank outsiders Togo, who are based in the city of Wangen, play their first Group G match against South Korea in Frankfurt on Tuesday.
Their other opening-round opponents are Switzerland on June 19 and France four days later.
The players had demanded 155,000 euros ($196,200) each to play in the tournament plus 30,000 each per win and 15,000 per draw. Officials from the small West African country said it was too much money.
Togo's Prime Minister Edem Kodjo had been called on to help resolve the pay dispute.
Pfister, who has also coached Zaire and Ghana, replaced Stephen Keshi on a short-term contract after Togo's poor performance at the African Nations Cup in Egypt at the start of the year.
The team failed to score a goal in those finals.
He guided Saudi Arabia through the France '98 World Cup qualifiers but was dismissed before the finals.
The German said he refused to allow meddling in his team selection by the Saudi princes and was pushed into a corner from which there was no escape.
Pfister has spent much of his life globetrotting, coaching eight different countries before Togo.
He spent most of his playing and early coaching career in Switzerland and has maintained a Zurich residence since 1959.