The Union government had last week banned the sale and purchase of cattle from animal markets for slaughter.
The environment ministry had notified the stringent 'Prevention of Cruelty to Animals (Regulation of Livestock Markets) Rules, 2017' under the Prevention of Cruelty to Animals Act.
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"We will challenge it legally. We will consult the state's Advocate-General on this matter. I will request the Centre not to interfere with the state's matter and destroy the federal structure," she told a press conference at the state secretariat.
"They (Centre) are an elected government and they have their jurisdiction. The state government is also an elected government and it has its jurisdiction," Banerjee said.
"It is a deliberate attempt to encroach upon the state's powers. It is undemocratic, unconstitutional and unethical. It is also an attempt to destroy the federal structure," she said.