No official reason for the investigation has been given.
But the Department of Trade and Industry has said it is looking into circumstances suggesting misconduct in the affairs of the company.
The news caused Guinness shares to tumble by 40p.
Inspectors arrived unexpectedly at Guinness’ London headquarters at 0930 GMT.
Insider dealing speculation
They have powers to force the company to produce documents but also call people to give evidence under oath.
The company was involved in a bitter takeover battle for control of the Distillers Group earlier this year.
Guinness won the Scottish Whisky Group for £2.6bn in the face of fierce opposition.
There is speculation in the City the inquiry has been called after revelations of insider dealing at the company.
The suggestion is that employees used privileged information of a future take over to buy shares for themselves or tip off others.
They later sold them after the share price rose.
Insider dealing is illegal but highly lucrative.
This is not the first problem to hit the City in recent months.
It was implicated in a scandal involving Ivan Boesky, an American, who made millions out of dealing in the shares of companies being taken over.
Information concerning his activities in Britain has been passed to the authorities in London.
Labour’s trade spokesman Robin Cook said he would be pressing the government for more information in parliament on 2 December.
MPs plan to debate the issue of insider dealing.
In 1987 four men were charged with an array of financial offences.
The case of the “Guinness Four” in 1990 was dubbed “the trial of the 20th century”.
Former Guinness Chief Executive Ernest Saunders was jailed for false accounting, conspiracy and theft.
Trader Anthony Parnes and businessman Gerald Ronson were jailed for false accounting and theft.
Financial consultant Jack Lyons was fined and stripped of his knighthood.
Their downfall was prompted by the arrest for insider dealing of Ivan Boesky.
In a plea bargain, he told US authorities of a share dealing arrangement organised to underpin Guinness’s stock price when it was pursuing Distillers, to trump rival bidders Argyll.