“Fifa is not involved in host country immigration processes, including visa adjudications, and has been informed by authorities that Mr Artan’s status will not be changed at present.
“In line with previous Fifa events, a host government ultimately determines who receives a visa and who is admitted into their country.”
Referees’ chief Pierluigi Collina has created a training hub for the tournament’s 52 referees and 88 assistant referees, in Miami.
All on-pitch officials must stay at the base in Florida for training, preparation and security.
It would therefore not be possible for Artan to stay outside the United States and only referee matches played in Canada or Mexico.
A senior adviser to Somalia’s ministry of youth and sports confirmed the denial of entry to the BBC and said Artan had been travelling with valid documents.
A Somali embassy official in Nairobi told the BBC that Artan’s diplomatic passport had been issued specifically to ease his travel after earlier visa difficulties.
Speaking in a statement to Reuters, Artan said that despite the circumstances he was in a positive mood and focused on the next challenge.
“I would like to thank Fifa and Caf for all their support and I promise to keep my refereeing levels up as I concentrate on the future,” he said.
“I want to thank the football family for their messages and wish my colleagues all the best success during the World Cup and I look forward to joining them again in future competitions.”
The Somali Football Federation (SFF) has contacted Fifa seeking urgent clarification.
Speaking to BBC World Service, Andrew Giuliani, who leads the White House Task Force on the World Cup, said: “While I can’t go into the derog [derogatory information] on that I can tell you it was the right decision by customs and border patrol and I support that decision.”
The World Cup runs from 11 June to 19 July.
An official in the Somali national football league championships, Artan became a Fifa referee in 2018 and has officiated at the Africa Cup of Nations.