The European Parliament is "totally ridiculous", EU Commission President Jean-Claude Juncker said in a heated outburst in Strasbourg on Tuesday.
Mr Juncker was angered by only around 30 MEPs attending a plenary session to discuss the Maltese presidency of the EU.
EU Parliament President Antonio Tajani berated Mr Juncker and asked him to show more respect, adding: "The commission does not control the parliament. It is the parliament that should be controlling the commission."
Mr Juncker responded: "There are only a few members in the parliament to control the commission. You are ridiculous."
- Video report by ITV News Political Correspondent Libby Wiener
The General Election results have left the European Parliament "unclear" what the UK's position on Brexit is.
While Theresa May spoke of a "hard Brexit" or even no deal in January, Brexit Minister Steve Baker told of the need for the "softest" Brexit on Tuesday.
A view seemingly echoed by Michael Gove who said the wishes of remain voters must also be taken into account.
Alyn Smith, the SNP Member of the European Parliament for Scotland, has pleaded with members to "not let Scotland down" after the country voted to Remain in the EU, in contrast to the UK overall.
Speaking in the European Parliament, he said: "There's a lot of things to be negotiated. We will need cool heads and warm hearts.
"But please remember this: Scotland did not let you down. Please, I beg you, do not let Scotland down now."
Sinn Fein MEP Martina Anderson has said if English votes "drag us out of the EU that would be like Britannia waves the rules", as she raised concerns over a border between Northern and the Republic of Ireland.
Speaking in the European Parliament, she said: "We accept, we respect and we will defend the wishes of the people of the north of Ireland.
"However if English votes drag us out of the EU, that would be like Britannia waives the rules.
"There was a democratic vote, we voted to remain. I tell you, that the last thing the people of Ireland need is an EU border with 27 member states stopped right in the middle of it."
French far-right leader Marine le Pen has hailed the UK's decision to leave the European Union.
Speaking at an emergency session of the European Parliament to discuss the fallout from the Brexit vote, the National Front leader told MEPs, "put away those sulky faces, put away those angry looks and rejoice in the free and great emancipation" of the British people.
She said she is "committed to pursuing the path of liberty" for France.
Nigel Farage has told the European Parliament the UK voted to leave the EU because a political union was imposed on them.
"The main reason the United Kingdom voted the way it did is because you have by stealth, deception, without ever telling the truth to the British or the rest of the people's of Europe, you have imposed upon them a political union," he said.
"And when the people in 2005 in the Netherlands and France voted against that political union, rejected the constitution, you simply ignored them and brought the Lisbon Treaty in through the back door."
Nigel Farage was greeted with jeers as he stood in the European Parliament - and taunted MEPs by saying: "You're not laughing at me now".
"When i came here 17 years ago and I said I wanted to lead a campaign to get Britain to leave the European Union, you all laughed at me," he said.
"Well I have to say you're not laughing now, are you?
"And the reason you're so upset, the reason you're so angry has been perfectly clear from all the angry exchanges this morning - you as a political project are in denial."
Nigel Farage and Jean-Claude Juncker embraced in the European Parliament on Tuesday, ahead of the first sitting since last week's EU referendum.
Later the European Commission President asked Mr Farage: "Why are you here?"