In a TV programme, the pioneer in DNA studies made a reference to a view that genes cause a difference on average between blacks and whites on IQ tests.
In 2007, the scientist, who once worked at the University of Cambridge's Cavendish Laboratory, told the Times newspaper that he was "inherently gloomy about the prospect of Africa" because "all our social policies are based on the fact that their intelligence is the same as ours - whereas all the testing says not really".
While his hope was that everybody was equal, he added, "people who have to deal with black employees find this is not true".
After those remarks, Dr Watson lost his job as chancellor at the laboratory and was removed from all his administrative duties. He wrote an apology and retained his honorary titles of chancellor emeritus, Oliver R Grace professor emeritus and honorary trustee.
But Cold Spring Harbor said it was now stripping him of those titles after he said his views had not changed in the documentary American Masters: Decoding Watson, aired on US public broadcaster PBS earlier this month.
Dr Watson became Cold Spring Harbor's director in 1968, its president in 1994 and chancellor a decade later. A school at the laboratory is named after him, the Associated Press reports.