Organisers of England's match against Italy appear to have tried to cover up dry grass at the Arena Amazonia by painting the brown patches green.
On Wednesday pictures emerged of the Manaus surface in a shocking condition thanks to over-fertilisation.
The grass was dry and brown patches scarred the surface, which will play host to England versus Italy on Saturday night.
On Thursday evening, despite an overnight thunderstorm, brown lines and patches were still visible.
A man with a cannister on his back appeared in the morning spraying what looked to be paint on the affected areas.
FIFA refused to comment on the idea that the brown patches had been painted, but they did confirm the pitch had undergone "treatment" ahead of Saturday's first Group D match in the northern city, which is located in the Amazon rainforest.
A FIFA spokesperson said: "The pitch in Manaus has been undergoing treatment in preparation for the FIFA World Cup. Over the last three months, mitigation procedures have been put in place and there continues to be, significant improvement.
"Pitch experts from FIFA and the LOC (Local Organising Committee) are satisfied that the pitch will be ready for training and the matches, and have been based in Manaus to ensure that all proper procedures are in place."
The Football Association said earlier this week that it had asked FIFA for updates on the situation.
One of England's backroom staff visited the stadium on Thursday to have a look at the surface.
In a fresh twist to the pitch debacle, the international players' union FIFPro condemned the state of the pitch at the £173million stadium, which holds 39,118 people.
"The players deserve a quality playing surface and conditions that reflect what is meant to be the world's premier football event. This is simply not the case in Manaus," a FIFPro statement read.
"Nobody wants to see the players and the spectacle in general suffer."
England landed in Manaus on Thursday ahead of their first Group D match.
Temperatures exceeded 30 degrees centigrade and humidity levels touched 60 per cent. The same conditions are expected on Saturday.
FIFPro is concerned that players' welfare will be put at risk during the World Cup, despite the fact that drinks breaks can be introduced if temperatures exceed 32 degrees Celsius.
"FIFPro's concerns stretch to parts of Brazil, including Manaus, where heat and humidity can reach dangerous levels at this time of year," the statement continued.
"Putting a player in harm's way is shockingly irresponsible and not how the game ought to be run.
"Cooling breaks are important - but when and how often they're introduced during a match is also open to interpretation in order to ensure optimal protection for the players."