The Brazil international, 25, is set to sign for Paris St-Germain for a world record fee, after telling Barcelona he wanted to leave on Wednesday.
La Liga officials believe PSG are violating Uefa's Financial Fair Play (FFP) rules.
But PSG do not think the issue will delay Neymar's transfer.
A senior source at the Ligue 1 club told BBC Sport's Richard Conway that La Liga was acting unlawfully, and that they are taking steps to resolve the situation.
The French league (LFP) says it is "surprised and does not understand" La Liga's decision and has asked its Spanish counterpart "to abide by the Fifa rules and its responsibilities".
A Barcelona spokesman told the Associated Press that they were "waiting to see how the situation develops".
The club said previously that they would report PSG to Uefa, European football's governing body, for a FFP breach.
In Spain a player must buy himself out of his contract.
This is done by depositing the amount of the buyout clause with La Liga - Spain's equivalent of the Premier League - to release the player from his contract. The league then passes the money to the selling club.
"We can confirm that the lawyers of the player have come to La Liga to deposit the clause and that it has been rejected," La Liga told BBC Sport.
FFP rules, first implemented during the 2011-12 season, stipulate that European clubs cannot outspend what they earn by more than 30m euros.
PSG are backed by money from Gulf state Qatar and La Liga president Javier Tebas has accused the French club of "financial doping".
He told AS: "La Liga is positing that state-backed clubs that compete using 'financial doping' could destabilise professional football in Europe".
Arsenal manager Arsene Wenger has criticised the deal, saying: "Once a country owns a club everything is possible and it becomes difficult to respect Financial Fair Play."
April 2016 - Rumours of a move away from the Nou Camp surface when Neymar's agent Wagner Ribeiro says the Brazilian striker has a £154m release clause in his contract which expires in 2018, and would discuss a move to PSG if the French champions showed an interest.
October 2016 - Neymar signs a new five-year contract until 2021, increasing his release clause.
May 2017 - Rumours resurface again after Barcelona end a disappointing La Liga campaign and Neymar fails to win the Ballon d'Or.
29 June 2017 - Speculation intensifies over Neymar's future as transfer window opens.
17 July 2017 - Reports emerge in the Spanish media suggesting PSG have met the player's release clause.
19 July 2017 - Barcelona club president Josep Maria Bartomeu tells BBC Sport Neymar will not leave.
20 July 2017 - PSG coach Unai Emery tells French daily newspaper L'Equipe they needed a player of the calibre of Neymar to compete with the big clubs.
21 July 2017 - Neymar posts an Instagram picture of himself in thoughtful contemplation, sparking a fresh wave of speculation.
23 July 2017 - Barcelona coach Ernesto Valverde shrugs off PSG reports, and tells reporters in New Jersey: "We want Neymar with us. We know his value on the pitch and what he brings to the locker room."
26 July 2017 - Defender Gerard Pique posts a picture of himself and Neymar on Twitter with the caption 'Se queda' ('He stays'). Pique later downplays the post, saying it was a "gut feeling" rather than a hard fact, but adds he hopes Neymar stays at Barcelona.
29 July 2017 - Barca striker Luis Suarez tells reporters in Miami: "As soon as he clarifies the situation it's better for us and him. He will have his say when he is ready and as a team-mate I will support him. Our relationship won't change. We want him to stay."
30 July 2017 - Neymar's Brazilian team-mate Dani Alves says he "hoped Neymar would join him at PSG" but insists he isn't using his personal friendship to sway the Barcelona forward's decision.
31 July 2017 - La Liga chairman Javier Tebas says he would file a complaint with Uefa for FFP breaches against PSG if any move is made for the player- "We will make a complaint to Uefa and if they don't do anything we will take it to the competition tribunals in Switzerland and Brussels. And, from there, we don't rule out going through the courts in France and Spain."
2 August 2017 - Neymar is given permission by Barcelona to leave after telling the club he sees his future elsewhere.
3 August 2017 - La Liga rejects an attempt by Neymar's lawyer's to buy out his contract.
* 222m euros is worth £200m at the time of writing (3 August). With fluctuating exchange rates, it was worth £198m when the story first emerged this week