Ali was booed by Indian fans at Edgbaston on Sunday, leading the all-rounder's father to suggest that the supporters' reaction may have been to do with his Pakistani background.
Porter initially suggested that Ali should take the abuse as a "positive", but has since apologised after receiving criticism for trivialising a potentially racially-sensitive issue.
"I would like to clarify comments I made in a telephone conversation with a reporter from the Press Association, which have been interpreted as meaning I do not regard racism as a serious matter," Porter said in a statement.
"I want to make it clear I believe racist attitudes and behaviour are unacceptable, at any level, in professional cricket, or in any walk of life.
"Moeen Ali has the full support of the PCA, as do all our members."
England won the T20 in Birmingham by three runs.