The special forces teams were formed in reaction to the September 11 attacks in the US and include a biochemical detection and reaction unit, a hospital team for patients affected by biological weapons and units operating the Vera passive monitoring radar system.
"It does not make sense for all the specialised units to function individually so we want to organise them so that their operation will be simpler and more efficient," Cirtek said.
But Cirtek denied a report on Czech national radio that the special forces would be scrapped altogether.
"We are not talking about losing any personnel or losing our specialist skills," he insisted, stressing that financial considerations were not behind the decision.
Cirtek said he did not know exactly how many staff were involved or when the reorganisation would be implemented.
The biochemical unit was called on by NATO to help protect the summer Olympics in Athens from an extremist attack.
The Czech army is currently undergoing a major reform aimed at making it fully professional. This includes ending conscription, axeing thousands of jobs and closing dozens of bases and plots.
The Czech Republic joined NATO in 1999 along with Poland and Hungary.