Reports stated earlier this week that the Premier League side had failed to land the 20-year-old after he was refused a work permit.
Despite suggestions that the deal was dead in the water, the Brazilian club have claimed that the breakdown in negotiations was due to a dispute over the option of a loan or permanent deal.
"It was said that he was denied [a transfer] but this is not true, the FA would only authorise the deal if it was permanent," Sao Paulo vice-president Joao Lopes told Globoesporte.
"The FA did not agree with the deal that was going on, so we will now meet again [wtih QPR] and try to come to an agreement."
Henrique is believed to be valued at £6m.