The Samoan government rejected the Sierra Leone team's attempts to enter the country for the Commonwealth Youth Games, which begin in Apia this weekend.
The Chief Executive of the Commonwealth Games Federation, David Grevemberg, says they asked Samoa to consider all options but ultimately the government is free to make it's own judgements.
"As the Prime Minister has rightfully said, he and his government, and of course their advisors and of course the advice they have sought, need to take into account what's best for the country, in terms of safety and security. We're very sorry for the athletes not being able to attend but this is something we're going to need to address with small states and island states as we move forward, but the Federation needs to respect the sovereignty of the state and what a government feels is in the best interests of their people".
The Commonwealth Games Federation rejected a proposal by Ghana to issue sanctions against Samoa, for denying Sierra Leone entry, at yesterday's General Assembly in Auckland.
In July this year, a foreign visitor to Samoa was forced to leave the country after being quarantined under Ebola protection measures.
The acting Director General of Health, Dr Robert Thomsen, says the traveller had visited the Ebola affected country of Liberia and came to Samoa through Australia before the required 21 days of clearance had been completed.
He says the woman had no signs of the deadly disease but the health requirements must be met.
She had left the country immediately after being quarantined.