Construction at Monks Cross was due to start this month, but developers Oakgate said the wet summer had seen a huge rise in newt numbers from just nine to an estimated 300.
Now Oakgate and contractor Caddick Construction must wait for the amorous amphibians to emerge from hibernation to trap and relocate the newts.
Building work on major stores for both John Lewis and Marks & Spencer is now expected to start in the spring.
The population boom was triggered by an archeology survey which left behind trenches which remained filled with water during the wet spring to provide perfect breeding habitats last season.
The shopping scheme will unlock funding for a 6,000-seat community stadium. Scheme backers said work on the new home for York City Football Club and York City Knights Rugby League Club will not be affected by the retail building delay.
Richard France, director of Monks Cross (Oakgate), said: “Naturally, I’m disappointed that work cannot start as early as we would have liked it to.
“However, as developers, we take our responsibility to the environment seriously and are making sure that all the newts are appropriately rehomed in line with our legal requirements.
“This delay does of course mean that John Lewis will no longer be able to open in 2013 as previously hoped for.
“However, assuming everything goes to plan, we expect the retailers to be open for trading in spring 2014. The timeline for the construction of the community stadium, being led by City of York Council, is unaffected.
“Once we get to start, our first task will be to prepare the site for construction, begin building the necessary infrastructure and then to commence building the new retail units, which include the new John Lewis, Marks & Spencer and Next stores.”