Santos have already turned down two official offers for the 18-year-old, who scored on hisBrazil debut in a 2-0 friendly win away to the United States on Tuesday, including one from Chelsea last month for 20 million euros.
The Brazilian club said they would only release Neymar for 35 million euros, the cost of rescinding his contract.
"The English club presented us with a formal proposal some time back after having begun direct talks with the player and his representatives," Santos president Luis Alvaro Ribeiro said.
"We refused it and made it clear we had no interest in negotiating the economic rights of this player who is under contract to Santos," he told reporters at the club.
"I found out that the siege continued. That's intolerable in view of the ethics that must govern relations between the clubs of world football," he added in his remarks posted on the club website.
"In accordance with FIFA norms, Santos will defend their interests to prevent this type of attitude contrary to (such) principles."
Santos said their lawyers were preparing a document on the issue to send to FIFA, probably on Friday.
West Ham United have also made a bid for the striker of 15 million euros that was also rejected by Santos.
Neymar is one of the biggest talents to have emerged in Brazilian football recently, shining alongside Robinho and Paulo Henrique Ganso at Santos this season.
He scored 14 goals in 19 matches as Santos won the season-opening Paulista (Sao Paulo) state championship and a remarkable 11 in eight games to help them win the Copa Brasil.