The two welterweight boxers have long been regarded as the best fighters in the world, but attempts to pair them up have always stalled.
Pacquiao's camp did not like the idea of random Olympic-style blood tests before the fight, which Mayweather demands of all opponents, and it is thought that money has also been an issue.
Mayweather, who was recently released from jail, has previously said that he would fight the Filipino legend.
"I don't have any hate towards Manny Pacquiao. I respect him, but I'm just saying it is not a crime," Mayweather told Hot97.
"I am also going to do random blood and urine testing, just so I can be in a clean sport - that's all I'm asking."
The unbeaten American also spoke of agreeing a financial package for the fight.
He continued: "We don't do the same type of numbers, so how can we split [50/50]?
"It's kind of hard. [Bob] Arum wants money but it's about putting the fighters in a good position. It's about Pacqiuao and Mayweather.
"If I do fight again, I will fight whoever they put in front of me."
Pacquiao himself is also deciding who to fight next. Rematches with Timothy Bradley or Juan Manuel Marquez could be easier to make than a bout against Mayweather.