The Competition and Markets Authority (CMA) believes the similarity of their services means the merger could reduce competition in the marketplace.
It warned that the deal could result in ‘worse terms for restaurants using either of the two companies’.
Just Eat, which processed a total of 88.1m UK orders last year, announced the £200m merger in December.
Though companies such as Deliveroo and UberEATS offer similar online food delivery services, the CMA said they represented less direct competition as they tended to target dine-in restaurants in fewer locations.
Just Eat said it was 'committed to demonstrating to the CMA that the market is, and will remain, competitive following completion of the proposed transaction'.
The company has until 17 May to offer its proposals to tackle the CMA’s concerns, or the merger will be subject to an ‘in-depth investigation’ by the authority.