Boris Johnson’s official spokesman said a “proper piece of work” is being done by civil servants, with their findings being reported to Number 10.
The revelation comes just two weeks after transport minister George Freeman told the Commons there was no work underway on the idea.
The Prime Minister first floated the proposal in an interview in 2018, saying: “What we need to do is build a bridge between our islands. Why don’t we? Why don’t we?”
And in a visit to a school last year he told pupils: “[I was talking yesterday] about building a bridge from Stranraer in Scotland to Larne in Northern Ireland – that would be very good. It would only cost about £15bn.”
However, critics have suggested the final bill for the 28-mile crossing would be far higher, and would have huge logistical challenges.
These include a million tonnes of munitions discarded in the Irish Sea by the Ministry of Defence at the end of World War Two.
Nevertheless, a spokesperson for the Prime Minister said: “This is an idea which the Prime Minister has expressed interest in in the past and I think he said at the time ‘watch this space’.
“The PM set out that this was an idea which he believed could have some merit. As a result of that you would expect government to be looking into it.
“Work is underway looking into it.”
He added: “The Prime Minister is ambitious in terms of infrastructure projects. He is looking at a wide range of schemes across the United Kingdom which could boost connectivity.”
The spokesperson went on: “Government officials are carrying out work in relation to the idea of a bridge linking GB mainland to NI.
“There’s a proper piece of work being carried out into the idea.”
Under the most likely proposal, the PM would seek to build a bridge-tunnel link between Portpatrick, Scotland and Larne in Northern Ireland.
A suggested model for the bridge is the Øresund Bridge and Drogden Tunnel which connects Denmark and Sweden.
The proposal has the support of Northern Ireland’s DUP, which included the bridge in its 2019 election manifesto.
Irish Taoiseach Leo Varadkar has also tentatively backed the idea, though he has insisted that Ireland will not foot the bill.
But critics have branded the bridge a waste of money, with some Northern Irish politicians calling for the money to be spent on local infrastructure investment.
Mr Johnson has previously been linked to a number of controversial infrastructure projects, including the scrapped garden bridge in London when he was the city’s mayor.
Over £46m was spent on the pedestrian crossing prior to construction, but it was eventually cancelled.
Other projects commissioned while Mr Johnson was in City Hall include the Routemaster buses, which cost £322m, and the Emirates Air Line cable cars which cost the taxpayer £24m but is only used by a small number of people.