The band issued photographers with contracts which demanded they surrender copyright of their images to the band. An improved contract was later offered, but still restricted editorial use of the images.
The National Union of Journalists are supporting the action, which will affect the three homecoming gigs at Heaton Park, North Manchester beginning tomorrow (June 29).
Freelancer Ian Tilton arranged the boycott, which is expected to involve hundreds of photographers.
John Toner, NUJ Freelance Organiser, said: "Too many musical artistes now wish to grab rights from photographers. Having said that, people are surprised that the Stone Roses have chosen to go down this route.
"We fully understand why a band would wish to retain merchandising rights, and the photographers would be happy to concede this. Equally, a photographer must have the right to license editorial use of images without obtaining the band's permission for each use.
[The Stone Roses performing at Spike Island in 1990]
"The band's intransigence on this point has led to the organisation of a boycott. The NUJ fully supports the boycott and will provide every assistance. We still hope, though, that agreement can be reached even at this late hour."
Tilton claimed that The Stone Roses were planning to "spring" the contract on photographers as they arrived at the gig. The document stated that the band would pay just £1 to obtain all rights to the images.
The Stone Roses performed their first comeback gig in Warrington on May 23.
Watch The Stone Roses in the video for 'Love Spreads' below: