All 14 Czech league teams voted against the agreement on Wednesday, reports the Associated Press.
The Russian clubs voted unanimously on Monday to reject the deal.
The new agreement increases the amount of compensation that the NHL pays to European federations for signing players.
Kozeluh said the Czech federation liked the pact in principle, but believed the minimum compensation payment of $150,000 for a player was too low. The Czechs also opposed the NHL's plan to pay in two installments.
In the new five-year plan, the NHL would pay $12.5million annually to a development fund managed by the IIHF — a $3.5million increase from the previous deal.
The IIHF distributes the money among the national federations and clubs that lose players to the NHL based on a formula devised by the IIHF and the national federations.
A player picked first overall in the NHL draft is worth $900,000, with each successive pick down to 30th decreasing by $20,000. Later draft picks are valued at $150,000 each.
The new formula was designed largely to satisfy the Russian clubs, which regularly lose their top prospects to the NHL.
