The French side are due to pay the striker five per cent of any transfer fee as part of his severance package.
But they are trying to avoid paying it on the basis that Gomis was involved in a sex scandal during his time at the club, according to The Times’ reporter Gary Jacob.
Lyon claim that the player’s arrest on suspicion of involvement in a gang rape last summer damaged the image of the club and that the pay-off should be waived.
Gomis and his representatives disagree with that assessment, and the French international was never charged with any offence.
The transfer is unlikely to happen until Gomis and Lyon reach on agreement on the pay-off.
The Magpies’ other main transfer target, QPR striker Loic Remy, was arrested in May on suspicion of rape and is currently on bail.