The DJ revealed that he turned down the opportunity to work with the star back in 2008 before she was a huge name, having to decline the work as he was busy.
However, GaGa misunderstood the quotes and quickly confronted Harris's claims, saying they were untrue.
"[I was] a bit surprised because it had been on Wikipedia for four years," Harris told Capital FM. "And I didn't say anything bad.
"I just said I didn't have time to do a remix – which frequently happens with all sorts of people. It's not really a problem.
"Something was taken the wrong way, or it was reported again, four years later, in the wrong way. But, it's just one of them things."
Harris is currently leading the UK midweek album chart with his new record 18 Months. The collection has also entered the Top 10 on the US iTunes store.
Watch the music video for Calvin Harris and Florence Welch's 'Sweet Nothing' below: