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Such matters are best resolved by applying goodwill, rapport, exceptional levels of persuasion, persistence, negotiation, reasoning, flexibility, adaptive skills……………..
You have posted that;
------“I work for small organisation with only ceo as my reporting manager.and few employees with no hr department.”
It does not mean that employee should get exploited.
Has this establishment registered under Shops and Commercial establishments Act of the state?
Does Payment of Wages Act, Standing Orders apply to it?
It should have displayed the registration certificate at a conspicuous place/near entrance/on notice board.
In this enactment in many of the states there is provision for issuance of appointment letter.
Appointment letter should be issued for upfront, transparent terms of appointment.
Even if appointment letter is not issued there are formats prescribed under this enactment which employer has to maintain.
If appointment letter is not issued there should be no notice period applicable to you as per agreed bilateral terms and conditions of appointment.
Under this enactment notice period is max. 1 month.
{The Inspector/Labor Commissioner may opine that notice period of more than 1 month is void.
Another employee has posted that Labor Commissioner opined notice period of more than 1 month may be termed void……….
https://www.lawyersclubindia.com/forum/Employer-not-relieving-employee-contt-89308.asp#.UkaBX9KAqWN }
You may maintain since the owner/CEO left he kept the office closed and ordered to remain at home.
--------“My manager went onsite and told me to take pay less leaves for approximately 3 months till he come back.’
Why should an employee be ignorant to this extent?
Did you apply for such leave in writing? Was it sanctioned?
Approach your lawyer and understand the merits and possibilities to raise and succeed in dispute for salary since the CEO left and closed the office and/or ordered to remain at home……………….If the office is closed why should employee apply for leave without wages.
---------“He is asking me what are your future plans? If you leave the job its loss to the company.”
What is the loss? Has it been proved and quantified?
The employee has been coerced/forced/mislead to write down leave application without wages……………………….and office was closed.
How can there be a loss?
--------“I am eligible for anual bonus, which he is denying to pay.”
If it is statutory bonus it should be paid by 30th Nov to avoid penalty/punishment…………………..
If it is not paid stake a claim for it and approach o/o Labor Commissioner if not paid.
First of all discuss the matter amongst elders in the family, competent and experienced well wishers, lawyer/law firm, trade union leaders and decide what exactly you want and on which terms of employer you can agree.
Try, negotiate and resolve.
You may find many other thread as relevant e.g:
https://www.lawyersclubindia.com/forum/Absconding-from-bpo-89455.asp#.UkaNU9KAqWM
If you are not able to resolve the matter then you may approach your lawyer/lawful authorities.