A criminal case was filed against me u/s 379 IPC and I was acquitted from charges of the same on 15 Aug 2016 . now three year passed can I file defamation case the said criminal case or I will be bared by limitation please guide

Barred by limitation period, but you can always pray for condonation of delay in moving for actionable claims.

The state moved on the basis of wrong information provided by a citizen and there was harassment.  Only an advocate can decide after going through judgment and other exhibits.  The limitation period starts from the date of providing the certified copy of the judgment.

Was the decision on merits holding the charges to be false or fabricated? Or is it that charges could not be proved beyond reasonable doubt?