Jack Smith, an independent special counsel appointed by the US attorney general to oversee federal investigations into Mr Trump, has charged the former president and two aides with “altering, destroying, mutilating or concealing an object” in connection with the case.
The updated indictment alleges there was a scheme to destroy surveillance camera footage at Mr Trump's Florida home.
The court filing claims that Mr Trump and his aides asked an employee to “delete security camera footage” to prevent it from "being provided to a federal grand jury".
The 2024 Republican presidential hopeful already faces dozens of criminal charges for obstruction of justice and making false statements about holding sensitive government files after his presidency ended in 2021.
The superseding indictment added a new count for wilful retention of national defence information, for a top secret document about plans of a US military attack on a country, which prosecutors claim Mr Trump shared with others not allowed to view it.
The document is thought to involve Iran, but the court document does not name the country.
"This is nothing more than a continued desperate and flailing attempt by the Biden Crime Family and their Department of Justice," the Trump campaign said in a statement.
Mr Smith also filed criminal charges against Carlos de Oliveira, a Mar-a-Lago maintenance worker, for his alleged role in helping Mr Trump to illegally hold on to the government files – making him a second Trump staff member charged in the case.
Federal prosecutors claims Mr de Oliveira talked to a Trump employee about the surveillance video footage and said that "the boss wanted the server deleted".
Mr Trump's aide Walt Nauta also faces criminal charges, and he has already pleaded not guilty.