Kenya captain Steve Tikolo said on Friday the players held a meeting with Cricket Kenya officials on Thursday where the dispute which threatened World Cup preparations was resolved.
Kenya will be in Group C in the West Indies with England, New Zealand and Canada.
"They agreed to pay us fees for the match against Canada which we were awarded after six of their players fell sick in Mombasa last month," Tikolo told Reuters by telephone from Nairobi.
Kenya won a tri-nations series against Canada and Scotland in the Kenyan Indian Ocean port city of Mombasa in January.
"They had said we were not going to be paid because the match did not take place. However, we insisted it was our right (to be paid) because we entered the field ready for the match, but the opponents did not come," said Tikolo.
"The ICC awarded us the match anyway. We demanded to meet them (Kenyan officials) before resuming training and we met on Thursday. They promised to pay us and we have agreed to resume training."
Cricket Kenya chief executive Tom Tikolo (Steve's elder brother) confirmed the meeting took place and that everything was agreed on.
"We will soon pay them and they have agreed to resume training. We don't anticipate any more problems," he said. He dismissed it as a minor issue that would not affect the team's World Cup preparations.
Tikolo (Steve) said Cricket Kenya had also agreed to draw up contracts for the entire squad, but said the terms were still not good enough to inspire a good performance from the team.
"The boys are just playing for the nation. But match fees of between $65 and $90 per one day international is still so low compared to what other World Cup squads are being paid," he said.
"We are currently living on match fees alone. No salaries and retainers, and to imagine that they wanted to withhold some of our money was too much to bear," he said.
Kenya were awarded $250,000 by the ICC for winning the World Cricket League which was played in Nairobi earlier this month and Steve Tikolo said the players had been promised $5,000 each from the winnings, while the rest would go towards development.