Ann Phoenix, of London's Institute of Education, said some pupils were disadvantaged by low expectations, sometimes from teachers who were "avowedly anti-racist".
"People talk about teacher racism disappearing but that is not true," she told The TES. "It is still there but often unrecognised by teachers themselves."
Professor Phoenix's view is based on her own research, which has involved talking to pupils in schools, and studies by other academics.
Progress had been made, she said, as overt racism was less common and the performance of ethnic minority pupils had improved. But she feared improvement for some groups had been too slow, pointing to research by her colleague Professor David Gillborn, which suggested that on current trends the "black-white" attainment gap would not close until 2054.
Professor Phoenix said: "One has to ask, 'Why does it continue?'"
Last year, a government report said there was "largely unwitting, but systematic racial discrimination" in schools.
Professor Phoenix, who tackled the issue during the annual King's College Education Lecture this month said teacher racism could take many forms. "Some of the overt examples of racism that existed in the 1960s and 1970s would be extremely rare now, apart from in some private schools maybe, but not in state schools," she said.
Today, less obvious examples, such as teachers being afraid to confront older black boys, were likely. In other cases, it could be as subtle as teachers' attitudes when pupils did not hand in homework.
"With some pupils, it might be demanded, and with others they might be very nice about it," she said.
Professor Phoenix said pupils could build up resilience to the problem by being confident in their skills, being determined to reach a goal or be the best, by knowing that their success was not impossible, and by having someone championing them.
Mary Bousted, general secretary of the Association of Teachers and Lecturers, said the test performance of some ethnic minority pupils was a concern.
"But rather than putting the blame on teachers who do very good jobs, let's do more to support those working in multicultural schools and more to reach out to different community groups," she said.