The Olympic celebration on July 27 now has a running time of three hours in order to help inexperienced G4S recruits cope with the deluge of fans, performers and athletes arriving at checkpoints, according to The Sun.
An insider added that the mass of animals being brought in for Boyle's 'British countryside' setpiece has further complicated matters.
"It's not just crowds of fans, athletes and performers G4S and our soldiers will have to cope with - it's dozens of live animals as well," they said.
"All will have to be checked and searched before being allowed into the secure area. It's a huge logistical challenge."
Boyle and his creative team are said to have complied with the cuts as they were concerned that fans would be stranded in Stratford, the site of Olympic Stadium, due to reduced transport services past midnight.
However, a London 2012 spokesperson has played down the changes to the ceremony, saying: "It's not a question of shortening the show - we're just trimming segments to keep them tight and concise so it all runs smoothly.
"It's a perfectly normal way to proceed when managing a production of this size. We're not aware of any problems with security."
Boyle previously apologised to performers after a number of opening ceremony details were leaked in the media.