British media said the female detainee was in her 30s and from Sierra Leone, one of the countries worst affected by the west African Ebola outbreak.
She was being held at the Dungavel House centre south of Glasgow, which is used to house unsuccessful asylum seekers before they are deported from Britain. The facility has a capacity of up to 200 people.
She fell ill and was taken to hospital to undergo tests.
"The results of the viral haemorrhagic fever (Ebola) tests which have been carried out are negative," said a spokesman for NHS (National Health Service) Lanarkshire, the local health authority.
"We can confirm that the patient does not have Ebola or another form of viral haemorrhagic fever."
The Home Office had suspended the detention or release of detainees from Dungavel while the tests were conducted. Staff and visitors were still allowed in and out of the centre.
The Ebola outbreak has so far claimed more than 1,100 lives in Sierra Leone, Guinea, Liberia and Nigeria.
The medical charity MSF has said the outbreak is moving faster than aid organisations can handle while the World Health Organization said the scale of the epidemic had been vastly underestimated.
The latest test in Scotland comes after an athlete from Sierra Leone, competing at the 2014 Commonwealth Games in Glasgow was tested and found to be clear of Ebola last month.