Can we use a specific primer or probe designed for Real time PCR as a FISH probe (off course with appropriate fluorophores)? Are there specific online software available for designing a FISH probe?
Yes you can design probes and primers for PCR. All you need is the idea of reporter and quencher but i guess that will be quite laborious to optimize.
In theory a PCR primer could be used as a FISH probe, however there is no guarantee that it will work. Different techniques have different requirements towards a good probe, e.g. the location of mismatches towards non-target sequences (primers should have them at the 3´end, FISH probes in the middle), so something that works with one method might not with another.
If you plan to use FISH probes for the detection of microorganisms based on 16S/18S rRNA then you should have a look at https://www.arb-silva.de/. The website has lots of information in regard to FISH probes and offers web-based and downloadable software for probe design and testing.
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