Commanders at the Fort Knox, Kentucky, post nixed Nugent's segment of a June concert after the rocker and conservative activist said at a recent National Rifle Association meeting that he would be "dead or in jail by this time next year" if Obama is re-elected.
Nugent told The Associated Press this week that his words were not intended as a threat against the president.
"To think that there's a bureaucrat in the United States Army that would consider the use or abuse of First Amendment rights in determining who is going to perform at an Army base is an insult and defiles the sacrifices of those heroes who fought for the U.S. Constitution, Bill of Rights," Nugent said.
Nugent said he had received messages of support from troops and noted that the Secret Service had met with him and closed its case about the remarks.
"There is nothing in my spoken word or written word that could be even wildly considered by any stretch of the imagination to be a threat to anyone," Nugent said.
In rallying support for Republican Mitt Romney, Nugent had said of the Obama administration: "We need to ride into that battlefield and chop their heads off in November."
Asked to clarify the remarks at the NRA convention, Nugent said: "A whole bunch of us ... believe ... we are in danger of being improperly and criminally jailed — I mean criminally on the part of the government."
Earlier in the week, Nugent pleaded guilty to transporting a black bear he illegally killed in Alaska, saying he was sorry for unwittingly violating the law.
He told the AP that he advises fellow hunters, "even when you are aghast at a maniac, inexplicable, illogical law, please abide by those laws at all costs."
Nugent said the prosecution in U.S. District Court was the result of a "witch hunt" by federal officials over his activism.
"We the people are turning up the heat," he said. "And that's why I'm being singled out by certain fish and game agencies and certain U.S. attorneys."