The world number one suggested on Sunday that male players should earn more as they generate more income.
But the Serb says he has been in touch with fellow players, including Murray, who criticised his initial stance.
"I never had any intention to offend them or come up with any negative connotations," he said.
The 28-year-old from Belgrade added: "I don't make any differences between the genders. I am for equality in the sport."
Djokovic said he had received a message from Murray on Tuesday and that they had spoken "very openly and frankly" about the issue.
The 11-time Grand Slam champion said he had also sent messages to Serena Williams, Caroline Wozniacki and Ana Ivanovic.
"I feel very sorry if, in any way, I hurt my female colleague tennis players," he said. "I have a very good relationship with all of them. I have a huge respect for all of them."
Djokovic had already apologised in a Facebook post on Tuesday to those people who may have been upset by his comments but went further when he faced the media in Miami on Wednesday.
That followed 30 minutes of discussions with Billie Jean King, a former world number one and founder of the Women's Tennis Association.
Chris Evert also spoke to Djokovic in Miami.
Evert, an 18-time Grand Slam champion, pointed to Djokovic's cultural upbringing as a possible reason behind some of his views.
"The Europeans were behind the Americans when it came to accepting equality," Evert said.
"I doubt you'd hear that as much from the American men players and I'm sort of applauding America for that."
Evert says the men's game has benefitted a lot from the rivalry of Djokovic, Roger Federer and Rafael Nadal.
But the American believes that the popularity of the men's and women's games is "cyclical".
"I know the women were bigger draws in certain eras, especially when we had American women at the top and European men at the top," she said.
"The last couple of years have been a golden era for the men's game because you've got three of the greatest players of all time."

William Carlin, 52, did not return to Castle Huntly prison near Dundee after a period of temporary release.
He was last seen near the city's King's Cross Hospital at about 09:00 on 5 November.
He has connections in Ayrshire and Newcastle, and Northumbria Police are helping with the search.
Carlin was jailed in 2013 after being caught with a security box containing Â£40,000 from a Sainsbury's in Prestwick.
He is described as 5ft 11in, with a slim build, short brown or grey hair and blue-grey eyes.
Police Scotland have warned members of the public not to approach him.

First Great Western has amended some services from midday to 20:00 BST because of the expected intense heat.
There will be no fast trains between London Paddington and Bourne End in Buckinghamshire or Henley-on-Thames in Oxfordshire.
Network Rail said if the track buckled the line must be closed for repairs "causing considerable disruption".
Trains from London Paddington will terminate at Twyford for a connection with a branch line service to Henley-on-Thames.
Passengers travelling to Bourne End will see their services from Paddington terminate at Maidenhead and will also have to complete their journey on a branch line train.
Temperatures are set to hit 30C (86F) in parts of the Thames Valley, the Met Office said.
Novak Djokovic has apologised to a number of leading female players - and spoken with Andy Murray - following his comments about equal pay in tennis.
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Police in Scotland and England are searching for a convicted armed robber who has been missing from prison for nearly two weeks.
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Hot weather is set to disrupt trains in the Thames Valley area with speeds being cut over fears of rails buckling.