Merchant Navy Day – introduced by the UK government in 2000 – is not listed as a flag flying day by UK Government Guidance.
https://www.gov.uk/guidance/designated-days-for-union-flag-flying
Merchant Navy Day is listed as a flag flying day by Scottish government guidance.
The Red Ensign is specified.
https://www.gov.scot/publications/flag-flying-on-government-buildings/
Merchant Navy Day is also celebrated by the Senedd Cymru.
The Red Ensign is specified.
https://senedd.wales/media/hl5dtuct/foi-574-final-redacted-response-saes.pdf
