The Stamford Bridge club have made a second bid of £21m for the 18-year-old Brazil international.
But despite the player wanting to move, Santos are holding out for the full £29.6m buyout clause in his contract.
"The club had sent us a formal transfer proposal, which was rejected immediately," he said. "But the harassment continues. Considering the ethics which clubs are supposed to adhere to this is completely intolerable, and Santos will go to FIFA to defend its interests.
"Yesterday there was a telephone enquiry. Chelsea got in contact with my secretary and asked for our fax number. This doesn't mean that they have opened negotiations."
The player's father Neymar Silva Santos: "The opportunity to leave Brazil is there. What I believe is that we have to think about valuing the player, not just the finances."