The Nigeria players failed to train on Thursday after reportedly demanding to be paid their bonuses for sealing qualification through to the second round of the tournament.
On the eve of their last 16 clash with France in Brazilia, Keshi confirmed that the situation had now been sorted.
"The premiums have been paid, there is no longer a problem," he said.
"It is not that we refused to train.
"We were awaiting a decision, we were in discussions with the federation, the time came and they forgot to go to training.
"We took the opportunity to put things right, the discussion was not only focused on premiums.
"We wanted a clarification and it was done. Everything is fixed now."
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