However, the head of the ICAI, Carlos Castresana, insisted that progress was being made and that police were close to shutting down a criminal network that stole drugs from organised crime.
Members of the network had stolen some 700kg of cocaine from a trafficker's warehouse in the town of Amatitlan and returned for another 350kg and an arsenal of weapons when they were ambushed by gangsters, Castresana said.
Five officers died in the April 2009 firefight that resulted in police seizing automatic weapons and about 500 rocket-launched grenades.
"We can't say whether it was the first or last time they had stolen drugs," Castresana said.
But he said authorities became suspicious of the slain officers after learning anti-narcotics agents blocked federal prosecutors from reaching the crime scene and noticing the national police did not open an investigation into the officers' deaths.
Police chief defence
In a brief meeting with reporters at a detention center, Gomez did not address the accusation that he was involved with a police group that was stealing drugs. But he denied he tried to cover up the involvement of the five dead officers.
"When that happened I informed my superiors," Gomez said. "These things happen in our country. We will appeal."
Bonilla called the accusations a vendetta against her, but she also did not specifically address Castresana's outline of the alleged crimes. "I have enemies and I was on their way," Bonilla told Channel 7 television.
At the time of the gun battle, police said it involved members of the Zetas, a group of hit men and drug traffickers linked to Mexico's powerful Gulf cartel.
The Zetas have extended their operations into Guatemala in recent years after coming under pressure from Mexican President Felipe Calderon's drug war.
Officials say Guatemala has become a trans-shipment point for cocaine heading north from Colombia, with Mexico's powerful drug cartels deepening their reach into the impoverished Central American country.
Guatemala has witnessed the arrests of a string of top law enforcement officials responsible with overseeing the fight against both local gangs and foreign cartels.
Bonilla is the second drug tsar to be detained and Gomez, who previously served as drug tsar, is the second national police chief to be jailed for alleged drug ties in recent years.
In September, Porfirio Perez, the previous national police chief, was suspended and later detained for allegedly stealing $300,000 from smugglers. He is awaiting trial.