The firm, TCB, won a contract to operate a new container terminal on Guatemala's Pacific coast for 25 years.
Mr Perez Molina was arrested in September after standing down amid anti-corruption protests.
He is due to appear in court next week. He and Ms Baldetti deny wrongdoing.
Attorney General Thelma Aldana said Mr Perez Molina started the approval process for the $225m project immediately after his election in November 2011. There were no competing bids.
Mr Perez Molina and Ms Baldetti "formed a criminal group", Ms Aldana added.
She made the announcement alongside the head of the UN-backed International Commission Against Impunity in Guatemala (CICIG), Ivan Velasquez, who headed the investigation.
The commission was set in 2006 to help Guatemala reform its justice system and confront criminal gangs that had infiltrated the state.
The Spanish executive in charge of the local branch of TCB (Terminal de Contenedores Barcelona), Juan Jose Suarez, has been arrested.
Mr Suarez said he had no idea why he had been detained, EFE news agency reported.
Mr Perez Molina resigned on 2 September and was arrested a day later. He said the contract offered the best deal for the country.
Anti-corruption protests had forced Ms Baldetti to stand down in May.
In a separate scandal, the two were accused of running a bribery scheme at Guatemala's customs, which became known as La Linea, or The Line.
A former television comedian with little political experience, Jimmy Morales, was elected president in the wake of the scandal.
Guatemala's former president Otto Perez Molina and his vice-president, Roxana Baldetti, took at least $25m in bribes from a Spanish port company, an anti-corruption commission alleges.