He added that officers should understand the viewpoint of politicians also as they were answerable to the electorate.
"You need not subject yourself to the pressure of political interference. At the same time I would request you to understand the compulsions of the politician," Mukherjee said addressing senior IAS officers attending a mid career training programme at the Lal Bahadur Shastri National Academy of Administration (LBSNAA).
Politicians have to go every five years seeking votes with a begging bowl and they were answerable to their electors, he said.
"We often hear the complaint that many a thing could not be done or implemented due to political interference. I do not hesitate to share the perception, yes it is there," the President said.
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Mukherjee recalled his first stint as a minister in the 1970s, saying he had a learned IAS officer as secretary whom he once asked if he felt "embarrassed" taking instructions from a newcomer like him.
He quoted his secretary's reply, "Mr Minister, when I receive instructions from you, I do not look at your face. I look beyond your face, the vast multitudes of people of this country who have chosen you to be here."