Multi-millionaire Harding said Buffett has a "habit of being right" but added that his own Winton Capital business, which manages more than $30 billion, offered lower fees and creditable returns to investors.
Buffett told investors last Saturday that low-cost index funds are a better option for most than paying higher fees to managers who often underperform, specifically hedge funds.
Harding is one of the first senior figures in the hedge fund industry to respond publicly to Buffett's comments.
"This is withering criticism of the active fund management industry overall, and it is hard to argue convincingly against," said Harding.
But Harding, who set up Winton in 1997, cautioned against tarring all firms with the same brush.
He argued that his Winton's funds have much lower fees than hedge funds are generally assumed to have and that the firm's risk-adjusted returns have been creditable. He did not give precise figures for returns.
Hedge funds made 5.51 percent on average in 2016, compared to losses of 1.12 percent in 2015 and gains of 2.98 percent and 9.13 percent in 2014 and 2013, respectively, according to data from Hedge Fund Research.
(Reporting by Maiya Keidan; Editing by Keith Weir)
By Maiya Keidan and Lawrence Delevingne