The Tigers will retain the 25-year-old's registration "in order to control any future compensation issues", but the 25-year-old has effectively torn up his reported £20,000-a-week contract which still had 18 months to run.
A club statement read: "It is in the best interests of the player and Hull City and he will therefore leave on a permanent basis.
"We would like to thank Kamil for his valuable contribution over the last three seasons and wish him luck for the future."
The Tigers paid Swiss club Young Boys £2.5million for Zayatte in January 2009 following a long-term loan spell.
City manager Nigel Pearson is understood to be close to signing Tunisia international midfielder Tijani Belaid, 23, following a recent trial.