They have come under fire from animal rights groups and Yarra Trams after a horse put its head through a tram window, but objections from the Melbourne Metro Rail Authority look like they might have reined in the carriages.

The authority confirmed it has told Melbourne City Council the carriages would present a safety risk during construction of the tunnel and station works in Swanston Street.

On July 14 a carriage horse driven by an unlicensed operator smashed its head through the window of a Swanston Street tram. The horse sustained minor injuries including a cut face.

A Melbourne Metro Rail Authority spokesman confirmed it has raised safety concerns about the horse-drawn carriages in Swanston Street as it planned for its massive construction project.

He said the authority was committed to allowing trams, pedestrians and bicycles access to Swanston Street during construction but it believed the horses and carriages presented a unique set of safety risks given the nearby construction site and other vehicles.

"It is just a question of safety," he said.

He said if approved within its current timelines works could begin as early as next year.

Horse-drawn carriage operators in the CBD have endured criticism including that they are dangerous to other road users, smelly and present a healthy hazard to the horses.

A Melbourne City Council spokeswoman said a note was sent to all horse-drawn vehicle operators recently stating that council was undertaking a review, and were seeking feedback on the future of horse-drawn vehicle operators following the expiration of current trading permits on February 2, 2017.

That feedback is due by July 29, and a report will then be presented to the Future Melbourne Committee in September, she said.

Horse-drawn vehicle operators and Melbourne Metro Rail Authority met on July 20 to discuss the project and its impact on Swanston Street between Flinders Street and Flinders Lane – the areas where horse-drawn vehicles currently operate.

"The intention of the meeting was for Melbourne Metro Rail Authority representatives to brief the horse-drawn vehicle operators," the spokeswoman said.

"The Melbourne Metro Rail Authority presentation identified that from the beginning of 2017, significant project construction works are planned for Swanston Street that will have significant logistical and access impacts on the existing horse-drawn vehicle parking and trading zones and the use of the section of Swanston Street between Flinders Street and Flinders Lane."

Classic Carriage Hire owner Alex Macdonald said he was working with council to determine the future of his business on Swanston Street.

But Mr Macdonald said he felt like carriages had been "rail-roaded" by the council and the rail authority.

"At the meeting with Metro Rail last week, carriages weren't even discussed. They're offering to pay out businesses like Hungry Jacks but they don't seem to care about us," he said.

Unique Carriage Hire owner Dean Crichton said that while he supported the works to Swanston Street, he was afraid council would not renew the industry's permits after February 2.

He said council should allow the carriage drivers to disperse to other parts of the city on a trial basis, rather than all gathering in one location.

"If we can't operate there we'll move on but that doesn't give council the green light to say get all carriages out of the city," Mr Crichton said.

"I can tell you this, that will not happen, they should let us move up into the city, further up Swanston Street, on Russell Street, Bourke Street, on a trial basis."

Horse-drawn carriages are not considered a motor vehicle by VicRoads and are not registered vehicles. But in much the same way as bicycles, they can use roads. It is understood that carriage operators do not need to have a driver's licence but must adhere to road rules.

Unlike segways and pedibikes, animal-drawn vehicles are legally granted permission to use Victorian roads as outlined in the road rules.

Melbourne City Council is still considering the future of all horse drawn carriages with a review, which is expected to form part of a Future Melbourne Committee report to the council on September 6.

The Melbourne Against Horse-Drawn Carriages group will hold its 11th protest against the carriages on Saturday.