Jose Manuel Barroso conceded he could not persuade MEPs to accept a line-up including his controversial pick for justice chief, Italy’s Rocco Buttiglione, a conservative who opposes homosexuality and believes women should remain in the home.
Dr Barroso said he preferred to make the necessary changes rather than face an embarrassing veto.
“If a vote is taken today the outcome will not be positive for European institutions,” he told the EU assembly to loud applause.
“I need more time to look at this issue.”
The vote was postponed after it became clear that most MEPs would vote against the new commission executive at the Strasbourg assembly.
But Italy is standing by its nomination of Mr Buttiglione as a commissioner, and the government of Silvio Berlusconi said it would talk to other European leaders to try to find a way out of the crisis.
The vote to approve the new commission has been postponed until Tuesday so Dr Barroso can choose a team the parliament would approve.
“Necessary changes and sufficient changes must be made in the team,” he said.
He said he would consult with EU leaders and parliament before putting forward new proposals “in the next few weeks”.
However Dr Barroso declined to indicate whether he is planning to reshuffle his commission line-up and place Mr Buttiglione in a less contentious portfolio, or ask Italy to propose a new candidate.
“I believe that stopping the clock is the best way to find a solution in the best interests of Europe and its people,” he said.
With the EU now entering uncharted territory, outgoing commission chief Romano Prodi confirmed he would stay on as a caretaker until the crisis is resolved.
Mr Buttiglione is a conservative Catholic with close ties to the Vatican, who has been outspoken in expressing his belief that homosexuality is a “sin” and women should stay at home to make babies.