He maintained that the government had to resort to the "extraordinary" route of Ordinances because "development cannot wait".
Naidu blamed the opposition for stalling bills during the last session of Parliament and appealed to them to let the House function effectively during the Budget session starting February 23.
"He (Mukherjee) said it would be better if Parliament runs smoothly and decides on issues accordingly. We are in agreement with the President's views," Naidu told reporters.
"People want development and there is a hunger for development. That is why it was necessary to bring the ordinances... That is why I appeal to all opposition parties to understand the advice given by the President," he said, adding, "Let us function effectively, debate and decide."
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Mukherjee had recently cautioned against the "Ordinance route" being taken for legislations, saying such action was meant for specific purpose "to meet an extraordinary situation under extraordinary circumstances".
A few days later, Mukherjee had said, "Enacting laws without discussion impacts the law-making role of Parliament. It breaches the trust reposed in it by the people. This is neither good for the democracy nor for the policies relating to those laws.