The revelation came Friday after Cohen's attorney's sought a temporary restraining order preventing the Department of Justice from viewing the documents, emails and other information they seized, citing attorney-client privilege.
In a filing Friday, prosecutors said "the overwhelming majority of evidence" is not expected to contain communications between Cohen and Trump.
"Cohen is not a criminal defense attorney, has no cases with the [U.S. Attorney's Office in the Southern District of New York], and is being investigated for criminal conduct that largely centers on his personal business dealings," the government filing said.
Prosecutors said they are using a team of investigators walled off from the main probe to sort through the material and remove privileged documents. Cohen's defense team, though, sought to review the material first.
U.S. District Judge Kimba Wood ordered Cohen's lawyers to produce a list of his clients and his lawyers by Monday. Prosecutors said they had at least one witness to confirm that Trump was Cohen's only client.
FBI agents raided Cohen's home, hotel and office Monday upon referral from special counsel Robert Mueller. The search doesn't appear to be directly linked to Mueller's investigation into whether Russia interfered in the 2016 U.S. presidential election or whether the Trump campaign colluded with Russia.