United boss Sir Alex Ferguson insisted Rooney - and team-mate Michael Carrick - caught viruses during the pre-season trip, where they played FA Cup winners Portsmouth.
But that triggered a backlash from the organiser, Bassey Ndem, who told The Sun: "They did not catch it in Nigeria.
"It's a lie from the pit of hell and it's sad someone had to go to that length to degrade Nigeria. Rooney only sat in his hotel room. He was in Nigeria for less than 24 hours."