Hi Rai,

You wrote:
I am very frequently reading the registers of the RTC(once every 1 millisec)...is this the cause for the problem.

Since the least significant data (10's seconds digit xx-xx-xX) is only changing once a second, why bother to read it 1000 times more than necessary? Just rewrite you code to read once a seconds and see if the clock runs more accurately. That will tell you where you problem lies.

Regards,

Charles Bannister