On Thursday, Chief Minister Mayawati ordered the closure of the shops citing reasons of law and order.
The stores are owned by the industrial group Reliance which opened 10 shops in the state capital Lucknow two days ago.
The opening saw protest demonstrations, and some of the stores were ransacked by a group of local traders.
A worried Ms Mayawati ordered the shutdown, saying she feared large-scale violence over the issue.
The opening of 20 other Reliance stores in the city of Varanasi has also been put on hold while the government reviews policy.
The Industrialists' Association of Uttar Pradesh plans to send a delegation to meet the chief minister.
"We would tell the chief minister to reconsider her decision," senior Reliance Retail official Manu Kapoor said in a statement.
On 22 August, a group of demonstrators set fire to two Reliance outlets in Uttar Pradesh. They were led by Banwari Lal Kanchal, an MP from the Samajwadi Party which is in opposition in the state.
Reliance stores sell fruit, vegetables and other food under one roof
Mr Kanchal says the traders will not allow the retail chains to function.
''We are against the entry of Reliance and other big companies in the retail sector as it will directly affect about 40 million people in the state,'' he says.
But the Reliance stores, which sell fresh vegetables, fruit, flowers and other groceries, are a hit with consumers.
Housewives in Lucknow, who found the retail outlets near their homes convenient to walk to, were upset to find them closed.
"I went to a retail shop to purchase vegetables, but the shop was being shut down," said one woman, Nisha Awasthi, who lives in the city's Gomtinagar district.
Across Indian cities and towns, brand new supermarkets are rapidly cornering a slice of what is a huge market.
Opposition to these stores mainly comes from the small traders and middlemen who fear that they will be edged out of the market by big supermarket chains like Reliance.
Reliance Fresh is owned by Bombay-based industrialist Mukesh Ambani who has announced that his company will invest $2bn (80bn rupees) in the agri-food retail network in Uttar Pradesh, India's most populous state.
Mr Ambani's estranged brother – Anil Ambani – is known to be close to the opposition Samajwadi Party.
After coming to power this summer, Ms Mayawati's government swiftly cast doubt over the future of a special economic zone Anil Ambani is planning in the state.