WASHINGTON—Emails on former Secretary of State Hillary Clinton’s private server contained national-security information classified at some of the highest levels, according to a new review by a government watchdog.

A letter from Intelligence Community Inspector General Charles McCullough finds that Mrs. Clinton’s email trove contains a type of highly classified intelligence information beyond “top secret,” referred to as “special access programs” or SAP. That designation is reserved for information shared on a need-to-know basis to protect intelligence sources, military operations or other highly sensitive government information.

In a separate review over the summer, Mr. McCullough’s office found “top secret” information on Mrs. Clinton’s home server. The new unclassified letter from Mr. McCullough to members of the House and Senate committees that oversee intelligence, reviewed by The Wall Street Journal, says that the intelligence community now believes even more highly classified information was on the server. The letter was reported earlier by Fox News.

Mr. McCullough’s latest finding is that “several dozen” emails in Mrs. Clinton’s archive containing information classified at various levels, including SAP.

Most of Mrs. Clinton’s email trove of about 55,000 pages from her time in office has been released by the State Department. That includes more than 1,300 emails with some information blocked out, or redacted, because it is classified.