In a joint statement on Sunday, Head of Public Service Francis Kimemia and Tourism Minister Dan Mwadzo said the Kenyan government had officially asked the U.S. embassy in Nairobi to lift Friday's advisory.
The officials say the terror alert hurts Kenya's massive tourism industry. Mombasa is a major destination for foreign visitors.
Kenya has often been on terror alert since sending troops into Somalia last October.
The Somali militant group al-Shabab has vowed to stage a major terrorist attack on Kenyan territory in retaliation.