[General] It has been a

1)It has been a wonderful experience working here.

2) I had a wonderful experience working here.

Can we use either of the above sentences when leaving organisation?

Yes.

You need to add "an" before "organisation".

1)It has been a wonderful experience working here.

2) I had a wonderful experience working here.

3) I have a wonderful experience working here. ( I doubt about this sentence)

Can we use either of the above sentences when leaving an organization?

I would use 1. 2 is OK, but 3 doesn't work for me.

You could say: I have had a wonderful experience working here.

suniljain said:

1) either of the above sentences

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I would use 'any' instead of 'either' because there are more than two.

Suppose I am working somewhere then can I say the sentence below:

I have a wonderful experience working here. If not, then whether it means that this sentence is not correct in any context.

It doesn't work for me.

If you're still working there, you can say "I am having a wonderful experience working here". If you've left the organisation, you can say "I had/I have had a wonderful experience ...".

suniljain said:

1)It has been a wonderful experience working here.

2) I had a wonderful experience working here.

Can we use either of the above sentences when leaving organisation?

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There's a difference. 1 means that working there was a wonderful experience. It explicitly means "working here" = "the wonderful experience".
2 could mean that while you were working there, you had a wonderful experience. It doesn't say what that experience was.

Therefore, I'd use 1.

You could also say, when aplying to a new job, the following:

I have the experience of working for a well-known company as a (for example) financial director.

For your new employer, that would simply imply that you have gained (most probably) the skills and knowledge required for that job.

Not a teacher.

Weaver67 said:

You could also say, when applying [STRIKE]to[/STRIKE] for a new job, the following:

I have [STRIKE]the[/STRIKE] experience of working for a well-known company as a (for example) financial director.

For your new employer, that would simply imply that you have gained (most probably) the skills and knowledge required for that job.

Not a teacher.

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Note my corrections above.

I prefer no.1. It sounds more natural and smoothy.
But i'm not a teacher.

Raymott said:

There's a difference. 1 means that working there was a wonderful experience. It explicitly means "working here" = "the wonderful experience".
2 could mean that while you were working there, you had a wonderful experience. It doesn't say what that experience was.

Therefore, I'd use 1.

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I have two doubts:

1) Does 2nd sentence doesn't explicitly says that nice experience was because of working in the organization. It means that nice experience may be because of other reasons.

2) I have a wonderful experience working here. What does this sentence means? is the sentence correct? I understand if the 2nd sentence is correct (as above) then this sentence should be correct. Am I right?

1) 2 does not specify that the wonderful experience was working there. The wonderful experience might have been a four-week affair with a secretary, which he had (no pun intended) while he was doing a boring job there.
2) No. "I have" is in the present tense. It's not right, and it wouldn't be natural even if it was.

You can't just arbitrarily use 'have' and 'had'.

Polyester said:

I prefer no.1. It sounds more natural and smoothy

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Use smooth. ;-)

It has been a wonderful experience of working here.

Is the above sentence in passive voice?

suniljain said:

It has been a wonderful experience of working here.

Is the above sentence in passive voice?

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Hello, suniljain.
It's not in the passive, unfortunately.

Do you know how to form the passive?
http://learnenglish.britishcouncil.org/en/english-grammar/verbs/active-and-passive-voice

It cannot be passive if the verb 'to be' is followed by a noun or an adjective.

Then is it present perfect tence?