You don’t report how many counters that must be managed, anyway I try to suggest some possible solutions at your question.
If you need a single counter you can use the counter on the SlimLine CPU module. It’s possible to read its value on a program executed on Fast task (Standard every 1 mS, but the time can be changed to your requirements and you can set times down to 100 uS). Here the screenshot of an example program, as you can see the program execution takes 9 uS and at the maximum 19 uS (Download program).
If you need more counters and for a significantly number of applications, we can modify the static output expansion I/O module. The module is based on a FPGA logic, so it’s possible to program it by adding up to 4 counters and the logic to preset a value and manage the output according to your requirements.