Boudou is the first sitting Argentine vice president to face such charges. He could be sentenced to between one and six years in prison, and be banned for life from elective office.
Boudou, who was on an official trip to Cuba when the ruling was announced, says he's innocent of the accusations despite evidence linking him to other defendants that was made public through investigative reports by Argentina's newspapers.
His defense attorney, Diego Pirota, called the judge's order "a fairy tale" and said he would appeal.
The charges against the vice president come at a moment when Fernandez is fighting other challenges. Economic problems recently forced a devaluation and court rulings in the United States threaten to force the country into default on its debts.
Still, Fernandez has remained loyal to her No. 2 even as the allegations have made him Argentina's least popular politician. His falling fortunes have left the government without a clear presidential successor ahead of the 2015 elections. Fernandez has yet to speak publicly about the case.
Potential opposition presidential candidate Julio Cobos said Saturday that the charges against Boudou reflect on Fernandez, and said he would seek to impeach the vice president.
According to the judge's investigation, Boudou — as economy minister and then vice president — acted to smooth the Ciccone Calcografica printing company's exit from bankruptcy and engineer its purchase by a shell company so he and other secret partners could benefit from unusual tax exemptions and lucrative government contracts.
The shell company, The Old Fund, was led by businessman Alejandro Vandenbroele, who is accused of secretly representing Boudou in business deals. The scandal broke open after Vandenbroele's former wife exposed the alleged arrangement, saying she had to give media interviews because her life was being threatened for what she knew.
Others who were charged Friday include longtime Boudou friend and business partner Jose Maria Nunez Carmona; Vandenbroele; former tax agency official Rafael Resnick Brenner; printing company co-founder Nicolas Ciccone, and his son-in-law Guillermo Reinwick.
The Ciccones have said Boudou was personally involved in the negotiations that persuaded them to sell 70 percent of the family company to The Old Fund.
Boudou has not denied signing a decree as economy minister that effectively erased the printer's debts by enabling the new owners to pay back taxes over many years at below-market interest rates.