Following his brief appearance before magistrates, Bridger was flanked by two officers as he was escorted back into Aberystwyth Police Station with a blue sheet over his head.
April was seen getting into a 4WD on the Bryn-y-Gog estate in the town of Machynlleth in Wales at 7pm on Monday.
Bridger was initially arrested on Tuesday on suspicion of abduction.
The one-time lifeguard was picked up on a main road not far from the river Dyfi. His blue Land Rover Discovery was found at a nearby repair garage.
As search teams began a fifth day of scouring the rugged terrain around the town, police announced they were working on the assumption that April was dead.
Detective Superintendent Reg Bevan told a press conference in Aberystwyth: "Mark Bridger has been arrested on suspicion of the murder of April Jones.
"The arrest does not detract from our efforts to find April and we remain committed to finding her. Her family has been informed and, as you would expect, they continue to be supported by a family liaison officer."
Looking tired and drawn, and sporting a pink ribbon to show his support for April's family, he renewed an appeal for information regarding Bridger's movements.
Another key area of the investigation has been the river Dyfi, where a small sonar vessel was deployed on Friday.
It can locate objects underwater and was seen skimming along waters 3.2km to the north of Machynllet.
Teams of sniffer-dogs, RNLI crews and mountain rescue experts have also been carrying out searches.
Another key location has been a farmhouse in the village of Ceinws, to which Bridger is believed to have moved around six weeks ago.
- AAP
