The team's mountain biking champion Mohamed Tholley was due to compete in the time trial event in Glasgow yesterday but failed to turn up, according to a report in the Telegraph newspaper.
However, Jackie Brock-Doyle, a spokeswoman for Glasgow 2014, said at a press briefing this morning: "We have not had a single report of any athlete that has gone missing.
"If someone didn't turn up and they had gone missing, they would have reported it to us."
Sierra Leone cyclist Moses Sesay, 32, was admitted to a Glasgow hospital last week after feeling unwell and doctors tested him for various conditions, including Ebola - which is blamed for 729 deaths in an outbreak in four west African countries.
But Sesay, whose homeland has declared a public health emergency, was given the all-clear and released from hospital in time to compete in the men's individual time trial at the Games yesterday.
Ms Brock-Doyle added: "If athletes have gone missing and their chef de missions are concerned they will talk to us and let us know.
"We haven't had a single report of an athlete that has gone missing."
Unisa Deen Kargbo, chef de mission of the Sierra Leone team, told the Telegraph: "Unfortunately one of our athletes has not turned up for his event and we do not know where he is. It is possible he is not coming back.
"The situation is very serious at home, and it is possible this is why he does not want to return. It is very bad there.
"We are all very concerned about what is going on, but the rest of us are determined to go home. The only problem is that it is becoming difficult to find flights."
Asked if there were any other athletes in isolation in Glasgow hospitals awaiting test results for Ebola, Ms Brock-Doyle said: "No, just to be really clear, there is no Ebola in the athletes' village, there is no Ebola virus in Scotland. I want to be really, really clear about that."
A spokeswoman for Health Protection Scotland also said it was an isolated incident and no other athletes were tested. ''No-one has tested positive for Ebola in Scotland,'' she said.
Commenting on how Scotland is dealing with any potential Ebola cases, Dr Colin Ramsay, of Health Protection Scotland, told BBC Radio Scotland: ''There's been no programme of actively screening athletes simply because of the Commonwealth Games.
''The situation is that if someone presents with symptoms suggestive of the possibility of Ebola virus infection and who has come from a country affected by the current outbreak - and that's Sierra Leone and Guinea and Liberia - they would be investigated accordingly and that would involve managing them with a set of standard precautions.''
He added: ''People in this sort of situation would be investigated for a number of conditions, not just Ebola. Sometimes people have more common diseases such as malaria so they are given a battery of tests to exclude all these diseases, but there are special tests that would be done for Ebola in these circumstances if someone has been in a country affected by the outbreak in the relevant period.''
He said steps have been taken to remind healthcare practitioners across the whole of the UK about being aware of Ebola infection, particularly in people coming from those affected countries and that guidelines are in place outlining how to deal with the situation.
Speaking later, Ms Brock-Doyle said: "Glasgow 2014 has spoken to the chef de mission to ask if he was concerned and wanted to report the athlete as a missing person. They said no, they are not concerned about the athlete's whereabouts.
"Until the athlete is reported missing and the chef de mission says they are concerned about the athlete there is nothing the organising committee can do because he has a valid visa to be in the country."