Beltran's positive test, which is the first in this year's Tour, showed traces of the blood-boosting drug erythropoietin (EPO), the French Anti-Doping Agency (AFLD) said.
He was 26th in the overall standings after Friday's seventh stage from Brioude to Aurillac.
Liquigas team manager Roberto Amadio said the 37-year-old would be withdrawn from the race although having imposed that sanction the Italian team will carry on.
"We are shocked and ready to take all the most severe measures if the 'B' sample comes back positive," Amadio was quoted as saying in a Liquigas statement.
It added that Liquigas would sack Beltran from the team with immediate effect if the 'B' sample is returned positive.
