Tariq Jahan's son Haroon was one of three men run over and killed in Winson Green, Birmingham, during the riots.
Mr Jahan met the prince and West Midlands Police and Crime Commissioner David Jamieson on Friday.
Buckingham Palace said it could not comment on Prince William's views, but the BBC understands he is sympathetic to Mr Jahan.
Haroon Jahan was 21 when he was run over and killed, together with Shahzad Ali, 30, and Abdul Musavir, 31, in Dudley Road, Winson Green, during the England-wide riots in August 2011.
A trial held at Birmingham Crown Court in 2012 found found eight men not guilty of murder and the judge said he found some police evidence "unreliable".
Mr Jamieson confirmed the prince had agreed to speak to the Policing Minister Mike Penning about the case.
Mr Jahan said: "The main thing that was said was that [the prince] was 100% behind the public inquiry."
He said an inquiry was necessary to get to the bottom of why the men were cleared.
"I want accountability," he said. "I want answers.
"I want to get to the bottom of it - what were the underlying reasons? Hopefully, in a public inquiry, we would get some answers."
He said the prince had told him to "go ahead" and tell the media of his support for the cause.
Mr Jamieson said: "Prince William, I am very pleased, to say met with Tariq Jahan and some of his family and showed them a lot of deep empathy
"I am very impressed at the interest he is taking in this case and his consideration to the family.
"I don't normally support public enquiries but on this occasion I am in favour of what Tariq Jahan is calling for because of all the different agencies that were involved."
Buckingham Palace said it could confirm the meeting had taken place and it was the third time the prince had met Mr Jahan.
"As it was a private meeting we can not divulge what was said," said a representative.
The father of a man killed during the 2011 riots has said Prince William  backs his demand for a public inquiry.