ABC News reported Tuesday the official, who requested anonymity because of the sensitivity of the subject, said full investigations were done, and in many cases there wasn't enough evidence to warrant prosecutions or discipline.
Former department investigator Aurelia Fedenisn claimed top officials tried to halt or delay multiple investigations that had the potential to harm the department, then led by Hillary Clinton.
The whistle-blower also claimed when the department's Office of Inspector General attempted to report on the alleged interference, that language was removed, ABC said.
The senior official, however, offered a point-by-point response to an internal Office of Inspector General memo, dated Oct. 23, obtained by ABC News, that detailed eight investigations by the investigative arm of the department's Bureau of Diplomatic Security.
The memo alleged senior officials had interfered with the investigations.
The cases included allegations an ambassador solicited prostitutes in a park near a U.S. embassy, that several members of Clinton's security detail hired prostitutes while on official travel, and that a drug ring was running near the U.S. Embassy in Baghdad, the memo said.
The senior State Department official claimed the language was removed because, when asked to provide evidence to back up those claims, the Office of Inspector General was unable to do so, ABC said.
"Tell us when and show us how," the official recalled saying. "Show me."
The network said an official from the Office of Inspector General recounted the sequence in a similar vein, saying the language was removed from the final report because there was not enough evidence to prove any wrongdoing.
The State Department has publicly denied any wrongdoing.
"We take allegations of misconduct seriously and we investigate thoroughly," spokeswoman Jen Psaki told reporters Monday.