The Brazilian, 25, is expected to sign for Paris St-Germain for a world record fee, after telling Barcelona he wanted to leave the club on Wednesday.
The 25-year-old was expected to complete his move on Friday and push to play a part in PSG's Ligue 1 opener on Saturday against Amiens.
However, Neymar's lawyer Juan de Dios Crespo had the cheque to trigger his €222m release clause rejected by the Spanish league on Thursday morning.
"We can confirm Neymar legal representatives went to LaLiga to pay buyout clause and it has been rejected," La Liga said in a statement. "That's all the information we are going to give for the moment."
The decision to reject the attacker's move - which looked all-but certain after he said goodbye to Barca players and staff on Wednesday and informed the club of his decision to leave - puts the transfer in a completely unprecedented situation, although the latest developments do not come as a surprise.
La Liga president Javier Tebas had already said that the organisation was going to reject that payment due to concerns over Financial Fair Play (FFP).
"Even if PSG do not meet the release clause we are going to report them," Tebas told Sport on Tuesday.
"We have already warned the president of Paris Saint-Germain that we would do so and we see that PSG's policy has continued in the same manner.
"They cannot invent some numbers where their commercial rights exceed those of Real Madrid and Barcelona. Nobody believes that."
Neymar's faith is now left hanging.
More to follow.