The DHSC sent a letter to the supermarkets formally requesting them to stop advertising and promoting the products, arguing the Tobacco Advertising and Promotion Act 2002 applied to all tobacco products currently on the market.
The Government said there was clear evidence of the toxicity from heated tobacco.
A Sainsbury's spokesperson said: ‘We offer a range of age-restricted products under our strict Think25 policy, including this heated tobacco device which is advertised. This is an alternative to cigarettes and is fully compliant with current legislation.
‘We recognise the deeply complex and emotive nature of this topic. We remain in close contact with the Government and industry partners and are planning our transition to ensure we also comply with planned incoming legislation.'
Morrisons said it was in the process of reviewing the DHSC's letter and would respond ‘in due course'.
The Tobacco and Vapes Bill, which is making its way through Parliament and is currently at the committee stage in the House of Lords, is expected to ban all tobacco and vape advertising and sponsorship.
Single-use vapes were banned by the Government on 1 June.