The Competition and Markets Authority said shoppers could face higher prices or a worse quality of service in places where both chains had shops.
It said it also needed to investigate whether a combination of Britain's second and third biggest supermarkets would have increased buying power over suppliers.
The merged company would overtake market leader Tesco and be better placed to defend against fast-growing German discounters Aldi and Lidl.
Sainsbury's has 15.4 percent of the market while Asda has 15.3 percent, according to Kantar Worldpanel's monthly data published on Tuesday. Tesco has 27.4 percent.
However, all of the "Big Four" chains, which also include Morrisons, are losing share to Aldi and Lidl.
Tesco is fighting back with the launch of its own discount store format later on Wednesday.
Both Sainsbury's and Asda, the British arm of U.S. retailer Walmart, had asked the CMA to move quickly onto the in-depth phase 2 stage, the regulator said in August when it started its inquiry.
The CMA said in August it was "vital to find out if the millions of people who shop in supermarkets could lose out as a result of this deal".
"We...will not allow it to go ahead unless any concerns we find are fully dealt with," CMA chief executive Andrea Coscelli said at the time.