The development follows probe against the 'two-minute' instant food brand across India over alleged presence of lead and taste enhancer monosodium glutamate (MSG) beyond permissible limits.
"We have issued circulars to all store managers to remove Maggi from the shelves since yesterday. The process is under implementation," Kendriya Bhandar Managing Director Jagdeesh Bhatia told PTI.
The order is for all the 130 Kendriya Bhandar grocery and consumer retail stores in and outside Delhi, he said, adding in Delhi alone there were around 100 stores.
It further said: "All the unsold stocks of Maggi (all variants) are to be returned to the concerned consumer godown for further necessary action."
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The Delhi government has banned sale of Maggi noodles and asked Nestle India to withdraw stock within 15 days.
Nestle's Maggi noodle has been at the centre of a raging storm after UP FDA tests found higher than stipulated levels of lead and MSG in it.
Several state governments have ordered similar tests.