The new development was announced by police at a press conference this morning.
Search teams are still looking for the missing youngster.
Police urged volunteers who had rushed to join the hunt around the west Wales town of Machynlleth to leave it to the professionals as the "dynamics of the search have now changed". April, who has cerebral palsy, has not been seen since Monday evening.
Bridger, 46, was initially arrested on Tuesday on suspicion of abduction. Announcing today's development, Detective Superintendent Reg Bevan told a press conference in Aberystwyth: "Mark Bridger has been arrested on suspicion of the murder of April Jones. He remains in custody at Aberystwyth police station, where he continues to be questioned.
"The arrest does not detract from our efforts to find April and we remain committed to finding her. Her family has been informed of this development and, as you would expect, they continue to be supported by a family liaison officer."
Mr Bevan spoke only briefly to reveal the development. Looking tired and drawn on the fifth day of searching, he renewed the appeal for information regarding Bridger's movements.
He said: "While this is a significant development in the investigation, I once again appeal to the public for information which may help us find April. We are looking to trace the movements of Mark Bridger between 6.30pm on Monday and 3.30pm on Tuesday and any sightings of him between these times.
"We also need information regarding the movements of the blue Land Rover Discovery, registration L503 MEP, between these times."
Superintendent Ian John acknowledged again that volunteer searchers had played a "vital part" in the hunt for April so far. But things have changed with the announcement that Mr Bridger is now being held on suspicion of murder, he said.
April was seen willingly getting into what is believed to be a Land Rover Discovery on the Bryn-y-Gog estate at 7pm on Monday.
Bridger, from Machynlleth, drives a Land Rover Discovery which was seized from a local repair garage on Tuesday and fast-tracked for forensic examination.
At the press conference, Mr John said that because of today's "significant development", it was no longer appropriate for the many volunteers who had joined the hunt for April to continue searching.
He said: "You have heard about a significant development in this investigation which has an impact on our search for April. We want to acknowledge, and are extremely grateful for, the efforts of the community volunteers who have supported the professional searchers in trying to locate her.
"They have been a vital part of our team throughout this search operation. Quite frankly, their commitment has been an inspiration to us all.
"The dynamics of the search have now changed and due to the passage of time and the developments within the investigation it is no longer appropriate for us to expect untrained members of the public to continue the search.
"So now we only require professional searchers to be involved in the ongoing search, which continues in and around Machynlleth."
The sombre mood of police officers at the press conference was mirrored among journalists. Both officers left the room in silence instead of waving away the usual questions from reporters for more information.
April's disappearance has prompted one of the biggest police investigations of its kind. Despite emotional and high-profile pleas for her safe return, no trace of the youngster has been found.
During the search operation, Dyfed Powys Police has deployed hundreds of specially-trained officers, many from other forces. The force helicopter has been used, as well as mountain rescuers and the Royal National Lifeboat Institution.
One key search location has been the banks of the river Dyfi, not far from where Bridger was arrested on foot on the A487.
His Land Rover was later found at a repair garage - prompting police to ask the public whether they had seen the 4x4 or its owner between 6pm on Monday and 3.30pm on Tuesday. They have asked if people had been contacted by, or spoken to, the suspect during these times.
Many residents of the close-knit town have begun wearing pink ribbons for April in response to an appeal from her family.
April was last seen getting into the car a few yards from her home, where she lived with mother Coral, 40, father Paul, 43, sister Jasmine, 16, and brother Harley.
Bridger attended the same school parents' evening as April Jones's mother and father just hours before the five-year-old disappeared.
The 46-year-old was seen at Ysgol Gynradd Machynlleth, where two of his children are pupils.
Witnesses saw the former leisure centre worker drive to the parents' evening, which started at 5pm, in his blue Land Rover Discovery.
A Powys County Council spokesman said: "I can confirm that Mr Bridger attended a parents' evening on October 1."
Sources close to Mr and Mrs Jones said the couple had been given a "glowing report" about their daughter's progress - and had allowed her some extra play time when they returned home as a treat. Just a few yards from her home, police said April was seen willingly getting into a large vehicle at around 7pm.