Perez, who took office in 2012 but was forced out after mass protests last year, used his position as president "to facilitate negotiations where he would obtain direct financial benefit in detriment to the interest of the nation," said prosecutor general Thelma Aldana on Friday.
Perez is accused of heading a "criminal network" that helped the Terminal de Contenedores Barcelona (TCB) firm win a 25-year contract to operate a new container terminal in Puerto Quetzal on Guatemala's Pacific coast.
Perez and former vice president Roxana Baldetti are in jail awaiting trial for allegedly heading a vast tax fraud network, which allowed companies import goods tax-free.
According to the new allegations, the contract with the Spanish company was signed in April 2012 and included $30 million (€26.5m) in commissions for local and international negotiators.
Perez and Baldetti allegedly walked away with $4.2 million each.
This was "a criminal group with clearly defined roles" led by Perez and Baldetti, Aldana said.
Spanish businessman Juan Jose Suarez, head of TCB's local affiliate, was also arrested, along with eight Guatemalans including a former cabinet official under Perez.
Perez and Baldetti are accused of conspiracy, passive bribery, money laundering and fraud, said Interior Minister Francisco Rivas.
Both Perez and Baldetti, scheduled to appear in court next week, deny the charges.