I have gone for prescan of our board to an semi anehoic chamber and we found that radiation mentioned by me above is due to a RGMII_TX/RX_CLK line which is 11inch long trace. RGMII_Clk line trace is made(11inch) intentionally to add delay of of 1.5/2ns which is required between data and clock line as per RGMII specification.
These lines are also going through a board to board connector.How we can reduce the radiation due to RGMII_TX_RX clock line?
To prove, that the (i guess microstrip) line is causing the emisions, I would replace it by a semi-rigid coaxial line of same delay. Generally, an open microstrip line has some radiative dispersion and may possbly make the ground plane radiate as well, depending on the board geometry. You should try to replace it by a lumped delay, e.g. a LC circuit, or a buffer.