On Wednesday, a group representing the Yanomami had said that up to 80 of their members had been killed by illegal gold miners.
Minister of Indigenous Peoples Nicia Maldonado said a team had travelled to the area by helicopter. She said they had failed to located the bodies witnesses had described finding.
"No evidence of any death was found," Ms Maldonado told state television.
Gen Jose Eliecer Pinto of the National Guard told the Ultimas Noticias newspaper that he had visited four indigenous communities along with other officials and that "everything is fine there".
A statement from a network of Yanomami groups had described how illegal gold miners had allegedly set fire to a communal house, and how witnesses reported finding burnt bodies.
Indigenous rights campaigners say the Venezuelan officials may have failed to find the community in question, which is based in a remote jungle location.