Hundreds of workers contracted to build the plant have been told they have no job after pipework subcontractor Redhall Engineering Solutions fell out with Vivergo.
About 25 police officers, along with two police horses, were sent to the site to ensure the protest did not get out of hand.
There were heated arguments as officers refused to allow protesters to get on to the construction site.
About 200 workers received a briefing by union officials before marching down from the car park at the top of the site down towards the gates.
They blocked the site entrance, resulting in queues of traffic, forcing vehicles to turn round.
Union bosses have blasted the actions of Redhall Engineering Solutions Ltd, Vivergo and project manager Aker Solutions.
None of the companies are accepting the workforce is their responsibility, with Redhall insisting the workers have been transferred to Vivergo under employment regulations.
GMB regional organiser Les Dobbs told the Hull Daily Mail: “The project managers have disowned the staff and are not taking social responsibility.
“There will be legal challenges and we are putting in place the grievance process.
“Feelings are running high. As far as we are concerned, Redhall is still the employer.”
Unite national officer Bernard McAuley said: “We had lengthy meetings all day on Monday and Vivergo are quite clear the workers remain in the employment of Redhall.
“We believe Redhall remains accountable for every employee and if it isn’t resolved, we will go to an employment tribunal.
“Work on the project will not restart now until at least June 11.
“We hope to sit down and talk with Redhall and Vivergo, but we have had no response so far.”
Vivergo said it is perplexed by Redhall’s claim that the workers have been transferred over.
A spokeswoman said: “The information Redhall has been saying is incorrect.
“We are a fuel company, not an engineering firm, so there is no reason for us to take on these workers. We do not hold the contracts.
“We sympathise with them and understand their frustration in not getting the correct information.”
Meanwhile, Redhall is seeking a meeting with Vivergo to clarify the situation.
A spokesman said: “We believe the employees have been transferred because Vivergo terminated the contract.
“We have twice contacted Vivergo in order to sit down and sort this out.
“We sympathise and accept the workers need to know where they stand.”
Redhall claims it is owed £14m after its contract was terminated by Vivergo which is a joint venture between BP, British Sugar and DuPont.
Redhall said it has completed 78% of the original contract plus variations and there are currently approximately £14m of costs on the contract unpaid.
Vivergo issued a statement saying they had cancelled the mechanical and piping works contract because the works “should have been completed by February 2011”.
The statement went on to say those works were “only 69% complete”