He is currently in a nursing home recovering from a car accident and is said to have "very minimal" awareness of his surroundings.
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.
Cold Spring Harbor Laboratory said the 90-year-old scientist's remarks were "unsubstantiated and reckless".
Dr Watson had made similar claims in 2007 and subsequently apologised.
He shared the Nobel in 1962 with Maurice Wilkins and Francis Crick for their 1953 discovery of the DNA's double helix structure.
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's statements are reprehensible, unsupported by science," the laboratory said in a statement, adding that they effectively reverse his apology.
