Why is energy lost in EM waves? I have read that accelerating charges lose energy through electromagnetic radiation. But no one explains the exact phenomena which takes place at atomic level. I understand why the accelerating charges radiate electromagnetic waves. But I dont understand why is energy lost in such EM waves.
I would clarify my question with an example. Suppose a ball moving with some velocity in vaccum hits another stationery ball then it would come to rest and the stationery ball would start moving. So this is understandable that the energy of first ball is transferred to second ball. I want similar intuitive explanation regarding EM waves. No equations please. I want an intuitive explanation.
 A: The underlying level of nature is quantum mechanical. . This means that electromagnetic waves are riding on zillions of photons, they are elementary particles in the standard model of particle physics.
Photons build up the classical electromagnetic wave in a mathematically complicated manner, but as light goes along, photons can interact with electric and magnetic fields on the light beam's way and leave the ensemble. 
Compton scattering is one of the ways, a photon may depart from the beam, but not the only way. Raman scattering, absorption , scattering from fields will contribute.
A: Our world is a world if interactions. Otherwise you and I would not be, would not know about this and could not interchange thoughts. So what are the carriers of the exchange?

Suppose a ball moving with some velocity in vaccum hits another stationery ball then it would come to rest and the stationery ball would start moving. So this is understandable that the energy of first ball is transferred to second ball.

Have a look on the surface of the two balls. It is composed of surface electrons. What do you know about the electric fields of two approaching electrons? They prevent the clash of equal charges. Also these fields interchange energy and the kinetic energy from one ball over goes to the second. The mediating particles are photons. So even for your example with the balls the carriers of the exchange are photons

I have read that accelerating charges lose energy through electromagnetic radiation.

EM radiation from accelerated charges in the meaning that this charges are isolated particles is only a special case of EM radiation. Our world is under the permanent emission and absorption of EM radiation and the absorption lead to emission again, this is called thermic equilibration. 
In the case of a mirror the incoming EM radiation in the visible spectra gets reflected mostly in the same range. For a black body the incoming radiation gets converted mostly to the infrared radiation. This happens due to dissipation of the incoming radiation to vibrations of the atomic constituents of the body and remission of IR photons.

But no one explains the exact phenomena which takes place at atomic level.

Our observations state that the thermic equilibration is reached if the incoming and the outgoing energy equals. Our observations state that for two comparable systems with thermic equilibration on the same level (temperature) the subatomic particles are in comparable states.
This means that the electrons - which are on discrete levels to the nucleus - of the both systems are distributed statistically on comparable levels. If such an electrons gets disturbed by an incoming photons it moves to a higher level but after this it looses this absorbed energy again in the form of a new photons and falls back into its main (for this temperature) level.

But I dont understand why is energy lost in such EM waves.

EM radiation is the emission of energy and it is the source for the absorption of energy. Both happens in detail in the form of photons, electrons emit and receive photons. So any EM radiation is an energy loss.
