Lets understand what happens during Meditation.
Owing to the repetition of a chosen word “SHAANTIHI” or any of your chosen mantra, in Meditation, centrifuging of the conscious mind takes place and there will be an inward movement of the conscious mind into its own subconscious layers. Then, what is hidden in the subconscious layers of the mind tries to come out in thought forms.
The subconscious mind is the storehouse of accumulated tensions, pressures and Karma (sum of actions and reactions) of innumerable past lives. Some of these hidden forces, depending upon the condition of the mind and body on a given day, are flushed out during Meditation in thought forms. It is just like digging a well where removing the mud is also a part of the process. Therefore thoughts during Meditation are not only natural but also an indication of the purification of the subconscious layers of the mind. So, thoughts are bound to arise during Meditation and grip your conscious mind till a related force is flushed out each time.
Thoughts are not at all a disturbance in Meditation but only an expression of the outgoing of negativity (tensions, pressures, stresses and karmic forces). Therefore, thoughts will be part and parcel of Meditation so long as the purification of karma is going on.
Thoughts are an integral part of Meditation. So neither encourage the thoughts because it indicates purification nor try to suppress them for the sake of concentration.
Whenever you realise that your conscious mind is on thoughts and not on the word “SHAANTIHI” in Meditation, bring back the attention of the mind on to the word “SHAANTIHI” of Meditation and continue repetition.
So long as release of tensions, pressures and Karma is there, thoughts continue to rise in Meditation, sometimes intense, sometimes moderate. Thoughts are an integral part of Meditation. So neither encourage the thoughts because it indicates purification nor try to suppress them for the sake of concentration. Be neutral to thoughts and just continue the repetition of the word of Meditation with easy concentration till the end.