The Mayor of London made the statement during an "Ask Boris" question and answer session on Twitter today (March 27).
Alberto Galloni asked: "Can you please support TfL taking over the SE London Metro lines & improve the service for us? We're Londoners too."
The mayor replied: "Yes absolutely this is the single best and most cost efficient way of improving transport in London."
Mr Johnson has made several calls for control of the capital's suburban railways to be handed over to City Hall.
A recent survey showed Southeastern had the joint lowest customer satisfaction levels in the whole country.
However, hopes of a takeover appeared to be scuppered last year after the Department for Transport delayed any decision on new franchises until 2018.
- UPDATE: Man dies after being hit by train near Grove Park station
- Nevermind the Tube strike - now Southeastern trains through Lewisham are cancelled
- Crofton Park broken down freight train causes Thameslink and Southeastern delays until 1pm
- Southeastern expects disruption again all day after yesterday's derailment
- UPDATE: Train derailment means no Southeastern service ALL DAY from Lewisham to Charlton