Mr Cameron pledged to leave the EPP in his 2005 leadership campaign
European Commission president Jose Manuel Barroso has said he "regrets" the Conservatives' decision to leave the European Parliament's EPP group.
Speaking after talks with Gordon Brown in Downing Street, Mr Barroso said he had spoken to David Cameron about the plan "on a number of occasions".
He said groupings like the centre-right EPP helped shape the EU's agenda.
The Tories hope to set up a new group, which party leader Mr Cameron said was a "profoundly" necessary change.
The Conservatives informed the European People's Party (EPP) last week that they intend to leave it in May.
The alternative bloc would be established after the European elections on 4 June.
To qualify as a grouping and get access to EU funding, the Conservatives would have to be joined by MEPs from at least six other countries - it is thought they will try to attract allies from the Czech Republic and Poland among others.
Mr Barroso said: "It is up to each party to decide in which European grouping it wants to sit. It is up to each party to decide, so I can't criticise a specific decision.
"But of course I regret that decision. My party is a member of the EPP and I regret this decision because in Europe [it is] the main political parties and the main political families that really shape the European agenda.
"On the Commission, we have members of the EPP, members of the socialist and social democrat family, we have members of the liberal family.
"As president of the commission, I am not party-orientated. I try to have a consensus approach. But of course these are the most influential families in Europe, those who shape Europe.
"I have discussed this issue several times with David Cameron so he will not be surprised to listen to me saying that I regret that decision."
Mr Cameron pledged to cut the Conservatives' ties with the EPP grouping during his 2005 Conservative leadership campaign, saying its federalist views were at odds with Tory policy.
But critics had questioned whether he would go through with it - partly because of the difficulty of finding sufficient allies from other countries to join any new group.
Speaking at his monthly press conference, Mr Cameron said: "On the EPP, I just believe profoundly we have got to have in politics a sense that, if we say something in Westminster, we say the same thing in Brussels."
He added: "I profoundly believe that we should be in the European Union but we don't want to see a further transfer of power from Westminster to Brussels."
Mr Cameron said the new grouping would "work closely with the EPP on all sorts areas where we agree", adding: "We will be happy neighbours rather than unhappy tenants."
On Wednesday, shadow Europe minister Mark Francois said he, shadow foreign secretary William Hague, and the Tory MEP leader Timothy Kirkhope had met EPP chairman Joseph Daul in Strasbourg.
"The meeting was amicable and during the course of it, we confirmed to Mr Daul our long-standing intention to leave the EPP and establish a new grouping in the European Parliament after the 2009 elections," he said.
The EPP was opposed to the UK having a referendum on the Lisbon Treaty - something the Conservatives campaigned for - and it wants closer economic integration in Europe, as well as common immigration, defence and foreign policies.
For Labour, Europe minister Caroline Flint warned last week that the Conservatives could put the UK "on the fringe of Europe" and undermine businesses.
For the Liberal Democrats, Edward Davey said it put the Tories "on the lunatic fringe of European politics".