The Serbian's comments followed inflammatory remarks by the tournament director Raymond Moore who suggested the women's tour had ridden on the 'coat tails' of the men's game.
Moore has since resigned.
Djokovic attempted to hose down the controversy in an open letter on Facebook but stopped short of saying he advocated equal pay for men and women in tennis.
"As you may have seen, I was asked to comment on a controversy that wasn't of my making," said Djokovic, who won his fifth Indian Wells title on Sunday.
"Euphoria and adrenalin after the win on Sunday got the best of me and I've made some comments that are not the best articulation of my view, and I would like to clarify them.
"Tennis helped me so much in my life and being where I am today, I felt the need to speak about the fairer and better distribution of funds across the board -- this was meant for both men and women.
"We all have to fight for what we deserve. This was never meant to be made into a fight between genders and differences in pay, but in the way all players are rewarded for their play and effort.
"This was my view all along and I want to apologise to anyone who has taken this the wrong way."
Djokovic's comments at Indian Wells were poorly received by leading players, with women's world number one Serena Williams describing them as "disappointing".
"I wouldn't say my son deserved more money than my daughter because he's a man. It would be shocking," Williams said at the Miami Open.
World number two Andy Murray said he supported equal pay "100 percent" and felt Djokovic's idea that pay should be linked to attendances did not stand up.
"It depends on the matches day by day. The men's game has had some great rivalries for the past few years," the Briton said.
"The whole of tennis should strengthen from that, not just the men's game."
(Editing by Greg Stutchbury)
