"The drugs - cocaine and heroin - had been confiscated in recent months during a variety of police operations. They had been kept in the department's basement premises pending a court ruling on their destruction," the newspaper said.
Internal affairs officers from Madrid have arrived in Seville to investigate the incident.
"The investigation will be focused on employees of the anti-drug and organized crime department," the newspaper said, citing internal affairs officers as saying that, "we are talking about corruption in police ranks."
A separate investigation is continuing in the case of a local police top official and two gendarmes serving in a village near Madrid who were detained in late June on drug trafficking charges.