The flagship ?10.5m ferry terminal at Liverpool's Pier Head has won the "Carbuncle Cup" which is awarded to Britain's worst new building.
Three judges for the Building Design (BD) magazine said the Merseytravel building was "a shining example of bad architecture and bad planning".
A spokesman for Merseytravel defended the building saying it had "tremendous community support".
"This is only the view of two journalists and an architect," he said.
The building incorporates ferry operations, a Beatles museum and a rooftop restaurant. It was designed by Belfast-based Hamilton architects.
The terminal is cantilevered on two sides and clad in limestone to complement the new Liverpool Museum next door.
The judges added: "It is such an amazing site, directly in front of the Three Graces, but the architects seem barely to have noticed.
"It is like letting a bad second-year student build next to St Peter's.
"The architect evidently once looked at a Zaha building in a magazine. It is essentially a horrible sectional idea that has been extruded like a stick of rock."
Judges were split between the Liverpool waterside building and a structure in Nottingham - both they said were appalling - but in the end they decided that "given the damage inflicted by the ferry terminal on what is a UNESCO world heritage site" it was the more worthy recipient.
Another of Liverpool's buildings - Cesar Pelli's One Park West - was shortlisted for the Cup.
The final three buildings that were nominated were: Make's Amenity building for Nottingham University, Hamilton Architects' Ferry Terminal in Liverpool and Queen Margaret University campus, Aberdeen, by Dyer Associates.