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The association said in a statement on Monday that "undermining the country's central bank was a recipe for disaster which the government must desist".
"Let the two talk and sort out the issues instead of the government trying to ride roughshod over the RBI, what they are trying at the expense of the nation."
Pitching for "effective independence", Mr Acharya had said the governments that do not respect central bank independence would "sooner or later incur the wrath of the financial markets".
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The central bank had earlier this month issued an objection to a government-led panel's recommendation for payments systems to be overseen by a regulator that would be set up outside the RBI's control.