Developers Watkin Jones and Son Ltd were given planning permission for the scheme in central Hull nearly two years ago, but were unable to deliver it because of the recession.
The company has submitted a fresh application seeking a further three years in which to build the apartments as the current permission expires next month, but this has drawn a series of objections.
In a report to the city council's planning committee, the Harbour Master said: "Any accommodation sited as close to the river edge as the plans would indicate will present health and safety issues for both the occupants and craft on the river, which is just 24 metres wide opposite International Bulk Liquids Lime Street depot.
"Any other craft sailing daily to the many other berths above Lime Street must squeeze through, often stern first, carrying hazardous cargoes such as diesel, kerosene and waste oil.
"A carelessly thrown cigarette end during one of these transits could prove disastrous, and there have been instances of rubbish thrown from windows, some of it deliberately aimed at passing craft, from student accommodation on High Street, where the river is much wider."
The Environment Agency has objected as no flood risk assessment has been carried out, and former committee chairman John Fareham, is among other opponents of the scheme – fearing the planned rise in tuition fees will reduce the demand for student accommodation.
Referring to the original application, he said: "The committee was told there was a demand for this and that was why they invited the developers to put their money where their mouths were and gave a limited time application.
"...With the indications of a shift in Government policy leading all commentators to suggest a reduction in the number of people this building is supposed to be for, there is a very real chance this will become another block of flats.
"If just another block of flats, it so flagrantly does not meet planning policy on vehicles that it will indeed be injurious to the character and amenity of the conservation area."
The development would see the construction of five buildings on the West Bank up to nine storeys high, comprising 104 apartments and 478 rooms, and off-street parking for 13 cars.
The report recommends the application is delegated to the city planning manager for approval, subject to a flood risk assessment being carried out.
The application will be considered by the committee on Wednesday.