Younger brother Andy was not even on the race after he had to skip it because of an injury amid growing discontent among the RadioShack-Nissan riders over unpaid wages.
Last year, Andy was second overall in the Tour and Frank was third before their Leopard Trek team merged with the strong RadioShack-Nissan outfit during the close season.
Also absent from this year's race is manager Johan Bruyneel, who, with his former protege Lance Armstrong, is facing an investigation by the U.S Anti-Doping Agency into alleged doping.
Andy Schleck has barely raced this year, failing to finish most of the races he has taken part in, notably pulling out of the Criterium du Dauphine when he sustained a sacrum injury in a crash.
Frank has also had little to show for himself this season, his best result coming in the Tour de Suisse when he took second place overall.
He was in 12th place overall in this year's Tour, with virtually no chance of repeating last season's podium finish in Paris.
"He's confident but does not know what is going to happen, he is on his way home," team spokesman Philippe Maertens said before the start of the 16th stage on Wednesday. "The team feel not so good this morning but how could you in these circumstances?"
Frank Schleck had failed a dope test for the diuretic Xipamide, his team said on Tuesday.
"We have faith in him but we can't explain that," Maertens said. "We're shocked."
RadioShack-Nissan sports director Alain Gallopin told reporters: "They told us that the substance was not on their list."
Xipamide, however, is on the list of the World Anti-Doping Agency's banned substances and is classed as "specified", meaning that Schleck's possible two-year ban could be dramatically reduced if he can prove that he took it inadvertently.
Frank Schleck pulled out of the Giro in May after his team said he had crashed although nobody witnessed an incident, prompting Bruyneel to publicly criticise his rider.
The Schleck brothers have sued their team over unpaid wages, along with Dane Jakob Fuglsang, and the International Cycling Union (UCI) said it was investigating the matter.
"Of course it has surprised us that the Schlecks and Fabian Cancellara complained to the UCI," Leopard spokesman Carlo Rock was quoted as saying in the Süddeutsche Zeitung earlier this week. "And Jakob Fuglsang has even sued us, the case is in court."
"I think there are great riders who have problems with the management," Gallopin said on Wednesday amid rumours that team owner Flavio Becca could pull the plug on the team.