While the first meeting was held days after the new government was formed, the second was after Diwali last year.
Wednesday's interaction, at the Panchvati lawns of 7 Race Course Road, the prime minister's residence, was followed by high tea.
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According to a statement by the publicity wing of the government, Modi termed the bureaucrats "one team". While he appreciated the work done by the team through the past 10 months, the recent coal block auction and the Pradahan Mantri Jan Dhan Yojana got special mention.
Modi asked all secretaries to work together, through consultation, to prevent a "communication gap". Any communication gap in this team was "untenable", Modi is learnt to have said. Officers in the government should have the freedom and protection for objective, honest decision-making, the prime minister said, adding efforts were being made to ensure this.