Melbourne faces "localised gridlock" on the West Gate Freeway after new roads to the Port of Melbourne are built, with average peak-hour speeds forecast to slow to a glacial 11km/h on some inner-city stretches of the city's busiest road.

The warning of looming gridlock near the port appears repeatedly in a series of reports and confidential briefings about the $1.6 billion Webb Dock project, which also reveal the project's costs are spiralling as VicRoads rectifies the botched road plans.

Among the serious planning mistakes was a failure by the port authority to design the roads for super-sized container trucks, which have had approval to travel on certain Victorian roads since 2013.

The omission means the direct freeway-port link has been built so that high-capacity trucks up to 36.5 metres long cannot use it and must travel several kilometres out of their way through residential Port Melbourne instead.

Traffic growth on the West Gate Bridge has also soared 8 per cent since it was widened to 10 lanes in 2011, an increase that was not factored into plans for Webb Dock.

The link was designed to funnel port-related traffic directly between Webb Dock and the freeway, reducing congestion and getting trucks off local roads. The design was based on a two-day traffic survey in 2010.

But a more up-to-date traffic modelling report, completed in October last year by engineering consultancy Aurecon​, found that the new roads have been designed in a way that will in fact make traffic worse.

Among Aurecon's findings were that by 2025, morning peak traffic on the West Gate Freeway would fall to 25 km/h on average after the new roads open, compared to 30 km/h if the road network was left as it is today.

In the evening peak, westbound traffic would move at just 11 km/h, compared to 13 km/h on average if no new roads were built.

The report did not consider Transurban's Western Distributor, a proposed alternative freeway crossing over the Maribyrnong River that is being assessed by the Andrews government but which had not been made public at the time. The proposal also includes a new connection between the Bolte Bridge and Webb Dock.

The flawed, $80 million road link between the West Gate Freeway and Webb Dock is already at an advanced stage of construction, but is set to be modified at an extra cost of at least $15 million before it has even opened to traffic.

These modifications will include duplicating Cook Street, the main feeder road into Webb Dock from the West Gate Freeway, and building an extra westbound entry lane from the port onto the freeway.

The roads fix is being handled by VicRoads but is to be paid for by the government-owned Port of Melbourne Corporation and is due for completion in late-2016.

Vince Punaro, VicRoads' regional director metro north-west, said the modifications would fix the unwanted scenario of pushing enormous trucks on to local roads and "accommodate 36.5-metre high-productivity freight vehicles to allow direct flow to and from Webb Dock".

But some other costs of the planning bungle could be borne by the future, private owner of the Port of Melbourne.

Confidential port authority briefing notes from December last year reveal the port is in dispute with BMD, the company it contracted to build the Webb Dock link, over who is to blame for the design failures.

The conflict has delayed construction of the link roads for several months while the port and BMD resolve a dispute over two gas and petroleum pipelines that have been unearthed during works.

The notes state the corporation has agreed to pay the pipelines' owners, APA and Viva Energy, for indefinite future costs they may bear because of the roadworks.

This includes a potential $200 million clean-up bill in the event of an oil spill into the bay.

The briefing notes state the pipeline owners have refused to bear costs in part because: "damage to Viva Energy's pipeline, which results in a petroleum leak is likely to be difficult to contain and will potentially cause severe environmental consequences (including the movement of petroleum into Port Phillip Bay)".

The port conceded that while the chance of damage to the pipeline is "unlikely, management acknowledges that the costs associated with this risk are likely to be high (in the order of $200 million) and potentially indefinite".

The Webb Dock container terminal is due to open in late 2016 or early 2017 and create capacity for the port to handle more than 1 million extra containers a year. The Andrews government is also seeking to privatise the port next year and use the lease proceeds to remove 50 level crossings.

The port expansion was initiated by the former Coalition government.

Concerns about whether the West Gate Freeway could cope with the extra traffic Webb Dock would generate have been raised by the state's freight industry.

Victorian Transport Association chief Peter Anderson warned in February that, "it'll be a bottleneck, it'll fair dinkum be a nightmare".