Metropolitan Police Commissioner Sir Ian Blair is "concerned and irritated" over claims journalists smuggled a fake bomb into Windsor Castle's grounds.
The couple will have their marriage blessed at the castle chapel
He said one officer had been moved from his post following a story in the Sun.
The paper claims two reporters drove a van past St George's Chapel, where the marriage of Camilla Parker Bowles and Prince Charles is due to be blessed.
"I do not want to pre-judge this but it looks as though somebody has done something pretty stupid," said Sir Ian.
"Perhaps it is a wake-up call, but I would not expect anyone in my organisation to need a wake-up call," he added.
Confirming there would be an inquiry into the claims, he said he expected Prince Charles' wedding to be a "very good operation".
He said he was doing "absolutely everything" to guarantee the wedding would be safe, adding the Met Police was the "premier force in the world" at dealing with big events.
The newspaper story comes just days after two tourists scaled a fence and entered a private castle area.
The Sun claimed it breached the castle's £5m security barrier with "breathtaking ease" and got to within a "stone's throw" of the Queen's apartments.
One of its reporters and a photographer say they drove up in a hire van with no security passes and no pre-arranged delivery time.
On board was a brown box marked "bomb" and the reporter says he had a fake delivery note.
WINDSOR SECURITY BREACHES
Feb 2005: Conman Michael Hammond, who posed as a senior police officer to get into Windsor Castle, is jailed
June 2003: Intruder Aaron Barschak jumps on stage dressed as Osama bin Laden at Prince William's 21st birthday
Nov 2003: Reporter Ryan Parry, who got a job at Buckingham Palace, claims security at Windsor is worse
1994: Security review launched after a ceremonial sword is stolen from the castle museum
1994: A pair of Eton schoolboys scale the castle walls and trigger alarms
After an attempt to check up on them failed, they were allowed to drive into the grounds - past the chapel where the royal couple will be blessed - and they were not searched, the paper said.
A spokeswoman for Buckingham Palace said: "Security is a matter for the police who have been asked to investigate."
Windsor Castle staff are already investigating how two men were able to enter one of its private areas last weekend.
Scotland Yard said the tourists were detected immediately and taken back to the public area but not arrested.
"The secure area of the castle was not breached at any stage", a spokeswoman said.
On Thursday Prince Charles was carrying out his last public engagement as a single man, visiting the London office of Breast Cancer Haven, a charity of which he is patron.
Weathermen are predicting the wedding, scheduled for 1230 BST on Saturday, will take place amid rain and chilly temperatures of 6C (43F).