"denied" requires an object. This is often a noun: "he denied the accusations", a gerund: "He denied having killed him", or a subordinate clause "He denied (that) he had killed him."
However, none of this is related to the perfect. "denied" is in the simple past. The same examples in perfect would be:
"he has denied the accusations"
"he has denied having killed him"
"he has denied that he had killed him"
"had killed" is in the past perfect - it happened before something else:
"He denied that he had killed him." in this case the act of killing happened before the denial.
"He has denied that he had killed him" - in this case the act of killing happened before something else, not specified in the sentence.
"Deny to" - is an archaic usage meaning to refuse : "he denied to pay his rent"