The two franchises had sought reduction on the ground that the BCCI did not fulfill the terms in the Invitation to Tender with regard to the number of matches this season.
They have already paid 75 per cent of the annual instalment of total fee amount, and had sought waiver of the balance.
However, the pleas were rejected in the Working Committee`s meeting here today.
Kochi and Pune franchises had argued that as per the contract, each team was to play 18 matches on a home and away basis, but the BCCI reduced the number to 14, and brought down the total number of matches from 94 to 74 to avoid a player burn-out.
Pune and Kochi franchises were bought with bids of USD 370 million and USD 333 million respectively. Franchises have to pay this fee in instalments, 10 per cent per year.
Meanwhile, sources said the issue of resting senior cricketers for the West Indies tour after a hectic cricket season did not come up for discussion during the meeting today.
India is scheduled to play a Twenty20, five ODIs and three Tests in the Caribbean from June 4-July 10.
The final of the ongoing IPL season, which began six days after the conclusion of the six-week long ICC World Cup on April 2, will be played in Chennai on May 28.