Mauricio Boraschi, the head of intelligence and security, presidential aide Irene Pacheco and Communications Minister Francisco Chacon resigned their posts this week, the BBC reported.
The BBC said Chinchilla used a jet owned by Gabriel Morales Fallon to fly to the funeral of former Venezuelan President Hugo Chavez. She also used it for a private trip to Peru.
Fallon has since come under investigation by Costa Rican authorities for possible ties to drug trafficking.
Fallon was "linked to very complicated and complex situations from a criminal point of view," Boraschi said earlier in the week.
Former Tico soccer player Rolando Fonseca said he is the one who coordinated the request for the plane, the Tico Times reported.
"On March 14, staff members from the Casa Presidential first contacted me to request a private jet to transport President Chinchilla to the funeral of Venezuelan President Hugo Chavez," Fonseca said. "The second time they [Casa Presidential staff] directly called the pilot to request the plane a second time to travel to Peru. He [the pilot] called me, and then I called the company's manager in Colombia, Carlos Arturo Espinoza Torres, to ask for authorization."