But the newly obtained case files point to a cover-up. They include cover pages from the inspector general’s office of the Security Ministry, which oversees the National Police. So if Mr. Chinchilla carries out a wide-ranging investigation to show that the government is serious about fighting corruption, it could end up ensnaring some of the president’s allies in the National Party, which has been in office since the beginning of 2010.

“There was a type of pact of silence,” said Thelma Mejía, a Honduran journalist. “These files passed through various police chiefs and they did nothing. They were known by various security ministers and they did nothing.”

The early fallout of the scandal is beginning. Foreign Minister Arturo Corrales, who had also served as the country’s security minister, resigned late Thursday. The first announcements of police firings are expected as early as this weekend. A civilian commission in charge of weeding out corrupt officers has asked for background on the nine top-ranked active generals in the police force, including José Ricardo Ramírez del Cid, a former police chief in 2011 who is named in the case files as the mastermind behind the assassinations.

According to the documents, Mr. Ramírez del Cid was one of the three who stayed behind the night before the antidrug czar was killed in 2009 to place the call to the drug lord. Another was José Luis Muñoz Licona, who was appointed police chief in 2010.

In interviews broadcast after the El Heraldo report, both officials denied any involvement in the assassinations. So did the police chief at the time of the antidrug czar’s killing, Salomón Escoto Salinas, who is also named in the documents.

The case files leave little doubt that inside the police, at least, the results of the investigation were known. In May 2012, an official in the inspector general’s office sent a copy of documents to the police chief at the time, Juan Carlos Bonilla, noting that he was acting under the orders of the security minister. At the end of 2013, Mr. Bonilla’s replacement as police chief, Ramón Sabillón Pineda, ordered special guards to protect the case files on both assassinations, as well as documents on other high-profile killings.