The endorsement follows a Billboard magazine report that independent music rights holders Beggars Group and Merlin Network signed royalty deals with Apple.
Apple's decision of not paying musicians had became a lightning rod for criticism in the music community. The iPhone maker flipped its decision on Monday following pop star Taylor Swift's move to hold back her latest hit album "1989" from the streaming service.
"Apple listened to our community and then revised its music service agreement, demonstrating that it is committed to treating fairly all creators - labels, artists and songwriters," said Darius Van Arman, co-founder of independent label Secretly Group.
Apple Music will launch at the end of June, offering subscribers a large catalog of songs for a subscription fee of $10 a month.
"Over the last few days, we have had increasingly fruitful discussions with Apple," said Martin Mills, chairman and founder of the Beggars Group.
"We are now delighted to say that we are happy to endorse the deal with Apple Music as it now stands, and look forward to being a big part of a very exciting future," Mills said.