While a user trying to clear GR/IR through transaction code F.03 clearing account, system prompts Message F5654: GR/IR clearing account cannot be manually cleared.

Solution:

You will get this message when you are trying to clear GR/IR account clear manually via Transaction Code: F-03). Normally GR / IR account(s) is / are cleared through F.13. You are getting this message because the GR / IR account has been setup for Post Automatically Only posting, which is preventing manual clearing. 

If you are looking for some solution to clear GR /IR Account through F-03, uncheck the Post automatically only.