Fabol said on its website that the players were protesting over unpaid wages at two first division clubs, Wilstermann and San Jose.
The domestic championship would also be halted, Fabol said.
"Apart from stopping the tournament, our players will not report to the national team when they are called up, that is our reality," Fabol's legal advisor David Paniagua told the Uruguayan radio station La Oral Deportiva in an interview.
"I hope we don't get to this extreme, but it's the responsibility of the directors. We don't want to keep extending the deadline. We have exhausted all the channels and there's a limit for everything."
Bolivia, who last qualified for the World Cup in 1994, are due to kickoff their 2018 qualifying campaign at home to Uruguay on Oct. 8 before visiting Ecuador five days later.
The Bolivian Football Federation (FBF) was thrown into turmoil when its president, Carlos Chavez, was arrested on July 17 on charges linked to an alleged scam involving a fund set up for the family of a fan who died at an international match.
Prosecutors claim the family never received any of the money raised by the fund.
Chavez, who is also treasurer of the South American Football Confederation CONMEBOL, is one of five senior FBF officials under investigation for corruption.
The FBF sacked Chavez last month, however CONMEBOL has refused to recognise the election in which a new board was elected.
Amid the confusion, former Bolivia forward Julio Cesar Baldivieso was named as new national team coach last month, only for his side to lose 7-0 to Argentina in a friendly on his debut.
"This is one of the worst moments in Bolivian football," Paniagua said.
(Writing by Brian Homewood in Berne; Editing by John O'Brien)
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