Dear Nicolas,
I can use RTT from /dev/rtc on AT91SAM 9263 board.
But the time get lost after power shut down . even 3 v battery is connected.

Please let me know whether RTT clock can run even in absence in case of
AT91SAM 9263 board ????

If not then let me know how I can connect DS1302 to the AT91SAM 9263 board??
What changes are required in kernel fiels and in which kernel files???

Most of the board producers are using an external RTC chip to the AT91SAM9263 board, if you need to learn why and how, you could refer to their design and their kernel patches.