Can i accpet cheque payment for selling my flat?

You may accept sale consideration through either banker's cheque or RTGS but don't accept customer's cheque as it may be dishonoured.

I concur opinion and advise of expert Sh. Bhartesh Goyal.

However, even if vendee insists upon cheque payment, get the same honoured, realised and transferred in your account before execution and registration of Sale Deed. 

Thank you all for the quick response. Will there be any tax implications for receiving the payment through Rtgs, NEFT or banker's cheque?

Contact and consult a tax consultant after closing this thread as you have adequately been advised for non-disputed issue.

Even if there is any other / funther query it is advisable to engage and consult a local prudent lawyer as you are getting benefitted with a huge amount by selling the subject property.