Paranaense rejected Leeds' initial offer of $5.6 million, after Elland Road representatives flew to Brazil earlier this week.
The club's president Mario Celso Petraglia has confirmed that they are now waiting for a new offer from Leeds.
The failed transfer of Robbie Fowler to Manchester City had led to speculation that the move for Kleberson would be called-off.
However, sources close to Leeds have maintained that the Kleberson deal is still on, but only if the ongoing problem with the fee can be resolved.
"We believe that the business will be concluded by the end of the month, which is when the registration period for Europe closes," said Petraglia.
"They tried to pressure us to sell Kleberson at the first price, but we are not in a bad financial position as people have been saying.
"There is not truth in that at all and so we will continue negotiations."
Kleberson, who has admitted he would love to move to Leeds, has already confirmed that he is prepared to stay with Atletico until the summer if his proposed move failes to materialise.
Meanwhile, Everton boss David Moyes has denied reports that The Toffees were ready to mount a rival bid for the player.
"Kleberson is somebody we have shown an interest in, but at present we won't be pursuing it," he said.
