Koubek said Czech football urgently needed to raise its technical standards to compete internationally following their return to the World Cup after a 20-year absence.
He defended dropping striker Patrik Schick, saying Adam Hlozek was preferred for his physical condition and suitability to the team's offensive strategy.
Koubek said heavy travel between venues, including flights to Mexico City, left players exhausted, questioning why Mexico were not required to travel to Dallas.
Midfielder Denis Visinsky was heavily affected by the high altitude in Mexico City, Koubek added, while many players arrived already fatigued from their club seasons.
"I have a contract and I don't give up any fights... I will definitely fulfil my contract," Koubek said when asked about his future.
"Czech football has been lagging behind, we need to improve our play... select players who can compete at this level," he said.
FIFA World Cup 2026
The 2026 World Cup is taking place from June 11th to July 19th in the United States, Canada and Mexico. The tournament features 48 national teams and is played at 16 modern stadiums.
Match schedule and times | Group tables | How to watch the World Cup | World Cup Format | Past winners of the World Cup