A ministry statement on Saturday says the warning is "baseless."
An embassy message earlier this week urged Americans to "elevate their situational awareness" when visiting the pyramids because of a "lack of visible security or police" presence there.
It noted incidents of "angry groups of individuals surrounding and pounding" on cars with visitors, sometimes trying to open car doors.
The ministry insists the pyramids' area in Giza, Cairo's twin city, is "totally secure" and that the overall situation for tourists has improved.
Security deteriorated following the 2011 uprising that ousted longtime ruler Hosni Mubarak and tourism took a sharp hit.