"Peter Hill will remain CEO of Sri Lankan until the contract expires in March 2008," a spokesperson for Emirates said.
Hill had been part of a core team that set up Emirates in 1984.
Sri Lanka's government owns 51 percent of the airline and it is the flag carrier of the island.
Hill's visa was revoked over a failure to accommodate on an over-booked flight a presidential delegation that was touring UK.
Hill has to leave Sri Lanka by December 28. Emirates is expected to run the airline at least until a management agreement runs out in March.
The 10-year agreement has not yet been renewed and negotiations were started in 2007 to extend the deal.
Relations between the government and Emirates have been rocky, and officials have said the terms of the current agreement were not favourable to the govern