The Brazil international moved to Camp Nou in June 2013 for a reported €57.1 million (£50m), although figures released by the Catalunya club's new president Josep Maria Bartomeu last Friday indicated the forward cost €86.2m (£70.8m), excluding wages.
However, Santos received only €17.1m (£14m) of the transfer fee, while €40m (£32.9m) went to Neymar Sr's company N&N - co-owned by the 21-year-old's parents - which has caused the Peixe to become curious about the finer points of his deal with the Catalans.
The Selecao star's former club are furious that Neymar's father will only verbally tell them details of the deal and are 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 SR 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 €40m, 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 them about Barca's offer in 2011.
The Blaugrana paid Neymar's father €10m (£8.2m) up front over two years ago - with the other €30m (£24.6m) 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 Sr 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 - third-party investors who have complained that they have not been given their share of the money by Barca for the player's sale - showed Brazilian media details on Thursday that suggested that the agreement breached their pre-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 Brasil, 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.