The Civil Aviation Authority [CAA] advised organisers of the Send Off For Mikaeel event that was due to involve the release of up to 1000 balloons on both sides of the Firth of Forth of ways to make the event safe.
The tribute to the Edinburgh three-year-old, whose body was found in woods in Kirkcaldy, Fife, was one of many set up after a huge public outpouring of grief.
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."
The joint tribute between the Fife and Edinburgh communities affected by the boy's death is still expected to go ahead but will be scaled back at the Cramond side of the event while in Kirkcaldy a candle-lit vigil is planned.
It is understood conditions included that up to 100 small balloons could still be let off but that organisers should keep in touch with air traffic control at the airport with regard to timing.
Mikaeel's mother, Rosdeep Adekoya, was charged on Monday with his murder and attempting to defeat the ends of justice.
She made no plea or declaration at Edinburgh Sheriff Court and was remanded in custody and committed for further examination.
She is expected to appear again in court on January 28.