Yorke tweeted yesterday that, "Make no mistake, new artists you discover on Spotify will not get paid. Meanwhile shareholders will shortly begin rolling in it. Simples."
Yorke then retweeted a series of statements from Radiohead producer Nigel Godrich explaining why the songs had been pulled.
Godrich said: "The reason is that artists get paid fuck all with this model. It’s an equation that just doesn’t work.
"Meanwhile small labels and new artists can’t even keep their lights on. It’s just not right… Plus people are scared to speak up or not take part as they are told they will lose invaluable exposure if they don’t play ball."
The pair had support from artist Four Tet, who tweeted: "Exactly… I had everything on my label taken off [Spotify]. Don’t want to be part of this crap."
Spotify, which has cashed in with a global partnership with Coca-Cola, offers a limited free streaming service, with unlimited music streaming across two tiers priced at £5 and £10 a month.
The brand claims the $250m (£166m) it made in payouts to rights holders last spring shows the "huge strides" it is making "as a sustainable revenue stream for artists".
Yorke and Godrich’s Twitter outcry prompted David-Andrew Wallach, Spotify’s head of artist services, to respond himself, via Twitter, saying: "Really sad that Nigel Godrich and Thom Yorke are worried about Spotify.
"We spend a ton of time talking to artists and I really hope that they will meet with us to have a conversation.
"Been working hard to make sure that Spotify is the most artist-friendly music company ever."
Spotify said in a statement: "Spotify's goal is to grow a service which people love, ultimately want to pay for, and which will provide the financial support to the music industry necessary to invest in new talent and music."