Mr Johnson expressed "solidarity" with fans saying they should be at the heart of any decisions about the future of the game.
A banner outside of the Trafford pub in Manchester
The government is "exploring every possibility, including legislative options", to stop the proposed European Super League, the prime minister has said.
Speaking after talks with officials from football's governing bodies, Boris Johnson said "no action is off the table" in seeking to block the formation of the league.
A Number 10 statement said: "The prime minister confirmed the government will not stand by while a small handful of owners create a closed shop.
"He was clear that no action is off the table and the government is exploring every possibility, including legislative options, to ensure these proposals are stopped."
Downing Street has not ruled out stopping players of the clubs involved in the breakaway European Super League getting work visas or withdrawing police funding for match days.
Fans' representatives also joined the call with the Football Association, Premier League and Culture Secretary Oliver Dowden, which came as the backlash against the proposed European Super League continues.
Downing Street said Mr Johnson expressed "solidarity" with the supporters, saying they should be at the heart of any decisions about the future of the national game.
Liverpool, Manchester United, Manchester City, Arsenal, Chelsea and Tottenham are among the 12 founding clubs of the breakaway competition.
Downing Street said it would welcome any club stepping back from the proposal to form a breakaway European Super League.
The prime minister's official spokesman said: "I think we're fairly unequivocal that we don't want this to go ahead in the current form, so we would welcome any club that wants to step back from this approach but I think, as far as I'm aware, that's speculation at this stage."
Downing Street also did not rule out speaking to ministers in Spain and Italy to co-ordinate efforts to prevent the league going ahead as planned.
The PM's spokesman said: "We are keen to speak to everyone involved in this, from other countries to the Premier League and others."
Education Secretary Gavin Williamson told Sky News earlier that the league had been "dreamed up by money men" and "must be stopped".
He said the government could implement legislation and sanctions to stop it going ahead but would first be encouraging the six clubs to "step back" from the proposals put forward.
Labour's shadow culture, media and sport secretary, Jo Stevens, said the proposal is "a real watershed moment for football" and that Labour will support the government in attempting to stop it from going ahead.
The party has written to the Competition and Markets Authority (CMA), querying whether the new league raises competition issues.
In response, the CMA has said it will be "carefully considering" the European Super League proposals.
UEFA, in a joint statement with the Football Association, Premier League, La Liga, and Serie A, criticised the plans and did not rule out legal action.
It also threatened to ban players from all other competitions at domestic, European, or world level, meaning they could be prevented from playing for their national teams.
Meanwhile, FIFA president Gianni Infantino said his organisation strongly disapproved of the plans.
He told the UEFA Congress: "We can only strongly disapprove the creation of the Super League, a Super League which is a closed shop, which is a breakaway from the current institutions, from the leagues, from the associations, from UEFA and from FIFA.
"There is a lot to throw away for the short-term financial gain of some. They need to reflect, and they need to assume responsibility."
Source: Sky News