One envelope was addressed to Defense Secretary Jim Mattis, who is traveling in Europe this week, and the other to the Navy's top officer, Adm. John Richardson, a defense official said.
The envelopes are being examined to determine whether they test positive for the deadly poison, the Federal Bureau of Investigation said in a statement. The mail initially caused suspicions because it contained a sticky substance, per a defense official.
The two envelopes were screened and tested for the toxin at a mailing facility which is not inside the main building but is nearby, defense officials said.
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The Secret Service spokesman said the agency was working with law enforcement partners to investigate the envelopes addressed to Trump and that all threats directed toward a Secret Service protectee "are treated seriously and fully investigated".
The packages never made their way into the Pentagon, but were flagged in a mail delivery building next door on Monday, the spokesman said. The envelopes did not enter the Pentagon itself.
Unintentional exposure to the substance, the government says, is virtually impossible. In both cases, an initial test came out positive for ricin.
It adds that when "made into a partially purified material or refined into a terrorist or warfare agent, ricin could be used to expose people through the air, food, or water".