Judge Miguel Angel Galvez said he considered it "prudent" to deny bail to Baldetti, whom prosecutors and a special UN investigative commission accuse of masterminding a customs bribery ring along with President Otto Perez.
Baldetti, 53, is accused of running a scheme in which businesses bribed officials to clear their imports through customs at a fraction of the actual tax rate.
Prosecutors accuse her of taking a 50 per cent cut on all illegally slashed customs payments, for a total of some USD 3.8 million between May 2014 and April 2015.
Baldetti resigned on May 8.
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She was arrested Friday at a private hospital where she had checked in for gastrointestinal and heart problems, then jailed at a Guatemala City military base outfitted with a prison for high-profile inmates.
The scandal has been dubbed "La Linea," for the hotline investigators say importers would call to access corrupt officials.
Investigators say their findings are based on some 86,000 wire-tapped phone calls that implicate both Perez and Baldetti.
The president, a conservative retired general in office since 2012, is not eligible to stand for reelection.
He has apologized for the fact that the graft took place on his watch, but denied involvement and rejected calls to resign before his term ends in January.