The Brazil international moved to Camp Nou in June 2013 for a reported 57.1 million euros, although figures released by the Catalunya club's new president Josep Maria Bartomeu on Friday indicated the forward cost 86.2 million euros, excluding wages.
However, Santos received only 17.1 million euros of the transfer fee, while 40 million euros went to Neymar's father's company N&N - co-owned by the 21-year-old's parents - which has caused Santos to become curious about the finer points of his deal with the Catalans.
The Selecao star's former club is furious that Neymar's father will only verbally tell it details of the deal and is taking the issue to the country's courts, while slamming the underhand tactics used by Barcelona to poach the player.
"There is a way we can know [if what Neymar's father is saying is true]," a Santos representative told Globo Esporte. "Santos made an agreement whereby we sent the documents and everything relating to the negotiation. Neymar’s father called me and told me he would come here. He revealed that there was a confidentiality clause, meaning that he could talk, but not show us anything. Santos are going to dispute that [legally] and we are waiting for a response.
"When you have a figure paid such as 40 million euros, what happens is that everybody is suspicious. We feel deeply upset by the statement made by Barcelona, because it wasn’t what we had negotiated."
Another unhappy party involved in the complex transfer is the DIS Group, which claims that Neymar had broken the terms and conditions of their deal by not telling it about Barca's offer in 2011.
The Blaugrana paid Neymar's father 10 million euros up front more than two years ago - with the other 30 million euros to paid following an eventual transfer - to ensure that he helped ease through the deal at the expense of other interested clubs, such as Real Madrid.
Santos president Luis Alvaro de Oliveira subsequently denied all knowledge of any 2011 dealings between Neymar's father and Barcelona, but the player posted a document on Twitter on Wednesday, which seemed to suggest the club chief had signed a contract acknowledging the agreement.
DIS Group - a third-party investor that has complained that it has not been given its share of the money by Barca for the player's sale - showed Brazilian media details Thursday that suggested that the agreement breached an existing contract with Neymar.
"The agent promises to communicate to DIS, in writing, within 48 hours from receiving any proposal received that proposes the transfer the athlete Neymar da Silva Santos Jr. to another football club," the clause, seen by ESPN Brazil, reads. "They must inform DIS about the club, the source of payment, the amounts being paid and the payment periods."
Neymar's transfer has also been taken to the courts in Spain, following a complaint from a Barcelona socio about the legality of the financial aspects of the transfer.