The Competitions and Markets Authority (CMA), which has the power to block deals if it believes consumers will have less choice, said Friday the companies had failed to address concerns the tie-up was anti-competitive.
Amazon led a c.£450m funding round in Deliveroo last May, though its exact investment was not disclosed.
The CMA is concerned the merger could discourage Amazon from re-launching its own restaurant delivery service in the UK, which could increase competition and potentially lower prices for consumers.
Amazon shut down its London meal courier service Amazon Restaurants in 2018 after less than two years.
The watchdog is also concerned the deal could reduce competition in the burgeoning convenience grocery delivery market, a space where both Amazon and Deliveroo are active.
The companies were given five working days to address the CMA’s concerns in December, but failed to do so.
The tie-up will remain paused while it is referred for an in-depth Phase 2 investigation.