A serial prankster arrested after handing Theresa May a P45 unemployment notice was accredited to attend the Tory conference, police said.
The prank raised security questions, with a senior Tory suggesting the perpetrator could have been a terrorist.
Guidance on the Tory conference website said all attendees must have approval from the party and are accredited by Greater Manchester Police (GMP).
GMP Chief Superintendent John O’Hare said: “Officers attended and the man was arrested to prevent a breach of the peace and was released a short time later.
“The man had legitimate accreditation which granted him access to the conference site.
“In light of this we will be reviewing the accreditation process with the Conservative Party.”
People entering the conference had to go through “airport-style” searches, he added.
Amid frantic scenes, Nelson was bundled out of the conference hall and through the exhibition stands by security staff at the Manchester Central venue.
He told reporters: “Boris told me to do it. He’s left me in the lurch.”
Nelson was later seen being led away in handcuffs and placed in the back of a police van.
Around the same time, a tweet from his official Twitter account appeared, saying: “Hi @BorisJohnson, I gave Theresa her P45 just like you asked.”
The P45 he handed to the Prime Minister gave the “Reason for termination” as: “Neither strong or stable. We’re a bit worried about Jezza.”
A Downing Street source said: “We expect that there will be a thorough investigation into what happened.”
The source declined to discuss the Prime Minister’s security arrangements.
Senior Conservative MP George Freeman, head of the Prime Minister’s policy board, said of the prankster’s interruption: “There should be some very serious questions, that could have been a terrorist.”
He added to the Press Association: “My understanding is he’s a comedian, he’s often used by the BBC, and questions will be asked about how he was allowed to get that close.”
A Conservative spokesman said: “In light of the arrest during the Prime Minister’s speech we are working with the police to review the accreditation process and security arrangements for party conference.”
Security firm G4S defended its role at the conference to critics on Twitter.
A G4S spokeswoman said: “We weren’t the security provider for inside the auditorium, just the conference perimeter, entrances and exits.”
In a statement Shaun Hinds, chief executive of Manchester Central, said: “At the time of the disturbance, conference security protocols were immediately enacted resulting in the individual being quickly ejected from the venue and handed over to GMP.”
Home Secretary Amber Rudd said she was “very disappointed” about the security breach.
“I am going to continue to follow what’s going on, it’s in the hands of the police and we will make sure we look carefully into how it happened to make sure it doesn’t again,” she told BBC Radio 4’s PM.