More than 1,000 people are expected to turn up to two events on the banks of the Forth tomorrow evening to remember the three-year-old.
His body was discovered in Fife on Friday after he was reported missing from his home in the north of Edinburgh.
Balloons were due to be released from Cramond Beach in Edinburgh and Ravenscraig Beach in Fife as part of the Send Off For Mikaeel memorial event.
But advice from the Civil Aviation Authority (CAA) said balloons could cause a safety risk if released from the Edinburgh site on the south bank of the Forth.
Cramond lies below a major flightpath for planes landing at Edinburgh Airport.
Balloons and lanterns can still be released from the north side of the river, the regulator said.
A CAA spokesman said: "We were contacted by the organisers of the balloon release to mark the tragic death of Mikaeel and have been working with them to ensure the event can take place safely.
"Because the location is very close to Edinburgh Airport and following discussions with the airport we advised the organisers that there would be a potential risk to safety if they were to release balloons from the south side of the river but that it would be safe to release balloons and lanterns from the north side of the river.
"We will continue to offer any advice and support we can."
Mikaeel's mother Rosdeep Kular, 33, appeared at Edinburgh Sheriff Court on Monday charged with his murder and attempting to defeat the ends of justice.
She made no plea or declaration, was remanded in custody and committed for further examination.
Kular is expected to make a second appearance at the court on Tuesday January 28.