The former Kilmarnock, Hibernian and Plymouth manager, 51, took control of the Cranes in 2008 but failed to secure qualification to the African Nations Cup throughout his five-year tenure.
Uganda are currently bottom of World Cup qualifying Group J at the halfway stage having taken two points from games against Senegal and Angola.
A statement published on fufa.co.ug read: "FUFA hereby informs the public that a notice of termination of contract has been given to the Cranes' head coach Robert 'Bobby' Williamson.
"The Emergency Committee of FUFA sitting today took the decision of notice in compliance with the contract of employment and other relevant labour laws of Uganda including the Employment Act 2006.
"The technical committee will later next week convene to discuss more details that will be made public at an appropriate time if found necessary."
Williamson played as a striker for Clydebank, West Brom, Rotherham and Kilmarnock before starting his coaching career at Rugby Park in 1996.