Former Prime Minister Rail odinga ordered the dredging exercise at the Indian Ocean stopped.
According to Raila who is also the AU High Representative on Infrastructure, the dredging is interfering with efforts to recover bodies of the two victims of Sunday Likoni ferry tragedy.
The victims Mariam Kighenda and her four-year-old daughter perished after their car reversed and plunged into the Indian Ocean.
"I want to give an order here that the dredging works stop immediately so that those who are working here can work without interference," said Raila.
Divers involved in the recovery exercise have also been complaining of poor visibility due to dredging thus hampering the exercise.
The dredging is being done to widen and deepen the channel so as to allow bigger ships to dock at the Mombasa port.
Raila was speaking after he met the families of the victims and visiting the channel.