The Government has said it would be "deeply worrying" if energy prices have been driven up through market manipulation amid an investigation into activities at BP and Shell.
Offices of Norwegian firm Statoil were also raided by officials on Tuesday, as the European Commission examined allegations of possible wrong-doing in the pricing of oil, petrol, biofuel and other refined products.
A Downing Street spokesman said: "The European Commission is investigating and we would expect any companies which it wants to talk to to fully comply with these investigations."
The Energy Secretary Ed Davey later told MPs that anyone found to have manipulated prices would face the "full force of the law."
The Commission said it had launched the investigation over suspected anti-competitive agreements related to the submission of prices to Platts, the world's leading oil pricing agency.
"Officials carried out unannounced inspections at the premises of several companies active in and providing services to the crude oil, refined oil products and biofuels sectors," the EU's executive arm said in a statement.
"The Commission has concerns that the companies may have colluded in reporting distorted prices to a price reporting agency to manipulate the published prices for a number of oil and biofuel products.
"Furthermore, the Commission has concerns that the companies may have prevented others from participating in the price assessment process, with a view to distorting published prices," it added.
The statement did not identify the companies involved, saying the inspections had taken place in two EU member states and one non-EU country.
The three companies confirmed they were subject to the inquiry.
A Royal Dutch Shell spokesperson said: "We can confirm that Shell companies are currently assisting the European Commission in an enquiry into trading activities.
"We are fully cooperating with the investigation," the spokesperson said, declining to comment further for legal reasons.
A BP statement also said the company was "cooperating fully" with the probe.
Statoil said the inspection, at its headquarters in Stavanger, Norway, had been carried out with the assistance of Norwegian antitrust officials. Norway is not part of the EU.
Statoil said the suspected violations may have been ongoing since 2002.
Platts said in a statement that "the European Commission has undertaken a review at its premises in London this morning in relation to the Platts price assessment process.
"Platts is cooperating fully with the European Commission's review."
The investigation - one of the biggest cross-border actions since the Libor rigging scandal - had no impact on the London-listed share prices of BP or Shell on Tuesday though Shell's value dipped by more than 1% early on Wednesday.
The Commission said even small distortions of assessed prices may have a huge impact on the prices of crude oil, refined oil products and biofuels purchases and sales, potentially harming final consumers.
It said EU officials were accompanied by their counterparts from the national competition authorities, and stressed that the fact such inspections had been carried out did not mean the companies were guilty of anti-competitive behaviour.
Speaking on Jeff Randall Live, Robert Halfon MP, who had previously expressed concern over possible market manipulation, said: "This is incredibly serious because the price of petrol and diesel has gone up by 60% over the last few years despite the fact that the Government has both cut and frozen fuel duty.
"This impacts on the lives of millions of people up and down our country, not just people who drive cars - it affects food prices and transport and business and everything else."