I see many Chabad centers around , is Chabad an Orthodox Jewish organisation ? And which major authorities (Like Chief Rabbinate of Israel) recognize them as such?
To clarify further , is Chabad an Orthodox Jewish organization or a Messianic one?
Let's pretend you asked this question in 1990.
Chabad-Lubavitch (Chabad refers to its philosophy, Lubavitch the town in Europe from which this sect originates) operates with their own brand identity, and the look and feel are occasionally a little different than what you'd see in most Orthodox synagogues, but the differences are minor enough that they'd be considered Orthodox. A person who converted through Chabad-Lubavitch, for instance, would be considered Jewish in almost all Orthodox circles. (However some of the practices s/he picked up may be a little bit different, so there may be a little bit of relearning if s/he wanted to fit in with the non-Chabad crowd. And that's okay. Plenty of people reaffiliate within streams of Orthodoxy.)
Note that some Chabad synagogues are designed as outreach centers, rather than a place the Chabad rabbi would choose to pray if he was visiting New York. So you might see prayers in English or the like. But if you ask any Chabad rabbi "what does an unadulterated prayer service look like", it will have the same core structure as any Orthodox service.
Now here's what's happened in the past few years that has troubled many folks in "mainstream" Orthodoxy: many Lubavitchers hoped that their grand rabbi, the late Menachem Mendel Schneurson, would turn out to be the Jewish messiah. Then he died. This effectively resulted in three streams of thought within Lubavitch:
This approach is entirely compatible with mainstream Orthodox thought -- it's basically reading right out of Maimonides' code of law.
Mainstream orthodoxy say these attitudes are philosophically wrong. (Now how wrong? It's possible there were Talmudic opinions that espoused something like them, but the majority has ruled otherwise.) While quite dangerous (it starts to look like another religion), most Orthodox rabbis have ruled that such beliefs are considered foolishness, but not technically heresy. (The list of such rabbis includes Rabbi Yehuda Hertzl Henkin, in a responsa published in Bnei Banim -- there's already a link to it here on J.SE; Rabbi Hershel Welcher, head of the Vaad of Queens (he's said it publicly repeatedly); and Rabbi Hershel Schachter (an acquaintance of mine in the pulpit mailed the question to Rabbi Schachter and received a written reply, which I saw).
Thus, a cow slaughtered by someone who doesn't believe in God is not kosher; but it would be kosher if slaughtered by someone who follows mainstream Orthodox theology but believes Rabbi Schneurson gets a second coming. And you can count such a person for a minyan.
At this point we've crossed a theological line.
So: minor difference in look, feel, and practice? No issue at all. Philosophy A about Schneurson? Entirely mainstream. Philosophy B? Rejected by mainstream Orthodoxy but not to the point of severing ties. Philosophy C? Beyond the pale. Now what percentage of Lubavitchers today espouse A vs. B. vs. C, and where are the trends headed? That's hotly debated today.