Officers searching for the missing Edinburgh youngster found a body in Fife shortly before midnight, it was announced today.
The body was removed from the scene before 4pm today for a post-mortem.
It was reported by Sky News and other news organisations that the person detained was Mikaeel's mother, named locally as Rosdeep Kular, 33, though police have not confirmed this.
Assistant Chief Constable Malcolm Graham said police "strongly believe" the body to be that of Mikaeel and that his family had been informed of the discovery.
Visibly moved, Mr Graham told a press conference: "The investigation into the disappearance of Mikaeel Kular has been wide ranging and fast moving.
"As a result of these inquiries I can confirm that we have recovered the body of a young boy in Fife shortly before midnight. We have informed the family and the investigation continues.
"A person has been detained in connection with the death.
"I would like to sincerely thank everyone who has shown such a fantastic response to the incident in terms of assisting the police with searches and in terms of our appeals for information and coming forward to assist with information.
"Without such vital assistance the police cannot do their job assisting those who live and work in our communities.
"As a result of this development clearly there will now be no requirement for any further help in relation to searches in the Drylaw area."
Mikaeel was last seen on Wednesday on Wednesday night when his mother put him to bed at their home in Ferry Gait Crescent at 9pm. She reported him missing after going to check on him at 7.15am the following day and finding he wasn't there.
The little boy, who had two sisters and two brothers, usually slept in the same room as his twin sister but was alone on Wednesday night.
His jacket and shoes were missing and police were looking into whether he might have left of his own accord.
Hundreds of volunteers from the local community joined emergency services in the search for the missing boy.
The body was found in Fife, a region north of Edinburgh across the Firth of Forth, but police have not disclosed exactly where the discovery was made.
The body is being left in situ for forensic and scenes-of-crime officers to carry out investigations, Sky News said, and would not be removed before morning.
ITV News said Mikaeel's family lived in Kircaldy in Fife before moving to Ferry Gait Crescent.
Forensics officers were yesterday carrying out a search of the family home.
Police also investigated a potential sighting of Mikaeel after a child matching his description was spotted in West Pilton Gardens, Edinburgh, at around 8.30am. The sighting was not confirmed as being Mikaeel.
It also emerged yesterday that he had not been seen at nursery since the Christmas break because he had been ill.
Hundreds of police officers were involved in searches, and were joined by specialist search teams, mounted officers, dogs, other emergency services and local organisations.
More than 200 volunteers, from firefighters to mothers wheeling prams, helped in widespread searches, with some scouring the foreshore of nearby Cramond.
Denise Fergus, the mother of James Bulger, the two-year-old who was murdered in Liverpool in 1993, tweeted her condolences.
She said on Twitter: "My heart is aching for that poor boy Mikaeel Kular brings it all back so sad."
Police have also said today that they are investigating an offensive comment made online relating to the disappearance of Mikaeel Kular.
The remark was made via social networking site Twitter by someone in the Greater Manchester area.
A police spokesman said: "Any reports of racist, offensive or abusive comments made online will be thoroughly investigated and those responsible will be brought to justice.
"If you commit an offence, we will investigate it and you will be prosecuted."