In rural areas, all shops, except those in shopping malls, are allowed to open.
In a late night order on Friday, the Home Ministry also said malls continue to remain shut but markets in rural areas can open.
However, opening of shops located in COVID-19 hotspot and containment zones, sale of non-essential items by e-commerce platforms and sale of liquor continue to be prohibited.
Amending its April 15 order, the Union Home Ministry said "all shops, including neighbourhood shops and standalone shops, shops in residential complexes, within the limits of municipal corporations and municipalities, registered under the Shops and Establishment Act of the respective State and UT" will be allowed to open during the lockdown.
The ministry also said shops located in registered markets located outside the municipal corporations and municipalities can open after following the drill of social distancing and wearing of masks but with 50 per cent of strength.
However, single and multi-brands shall continue to remain closed in these areas also.
"All shops registered under the the Shops and Establishment Act of the respective State/UT, including shops in residential complexes and market complexes, except shops in multi-brand and single brand malls, outside the limits of municipal corporations and municipalities, with 50 per cent strength of workers with wearing of masks and social distancing being mandatory" will be allowed to function.
In a statement on Saturday, the home ministry said the order implies that in rural areas, all shops, except those in shopping malls are allowed to open.
In urban areas, all standalone shops, neighbourhood shops as shops in residential complexes are allowed to open. Shops in markets and market complexes and shopping malls are not allowed to open.
"It is clarified that sale by e-commerce companies will continue to be permitted for essential goods only.
"It is further clarified that sale of liquor and other items continues to be prohibited as specified in the National Directives for COVID-19 management," it said.
Liquor shop licence is given under the Excise Act of the states while those shops which are allowed to open operate under the Shops and Establishments Act of the states.
"As specified in the consolidated revised guidelines, these shops will not be permitted to open in areas, whether rural or urban, which are declared as containment zones by respective States and Union Territories," the statement said.
The lockdown was first announced by Prime Minister Narendra Modi on March 24 in a bid to combat the Coronavirus endemic.
It was further extended till May 3.