P&O Ferries say its Liverpool to Dublin service has been "indefinitely delayed" after its vessel was prevented from leaving the English port.
The company has said Peel Ports presented the ferry company with a sudden demand for payment of almost £600,000.
In a statement, Peel Ports said that "any decision to detain a vessel is always taken as a last resort" and only when there was a "significant debt to repay".
The vessel carries food, medicine and other supplies between Liverpool and Dublin.
BBC News NI understands some of the freight is destined for Northern Ireland.
Peel Ports is the owner of The Mersey Docks and Harbour Company, which operates the docks at the Port of Liverpool.
A spokesman for P&O said: "We have been in open discussions since this crisis began with all of our ports and network to ensure that we can manage payments while everyone deals with this unprecedented situation.
"We had asked for flexibility in the time required to pay but the Liverpool port refused to respond, even though we were committing to full payment."
The spokesman added: "The irresponsible and unnecessary actions of The Mersey Docks and Harbour Company Limited at a time of national crisis have closed an essential Liverpool-Dublin supply route, which means vital goods will not be able to flow between the UK, Ireland and Europe."
A spokesperson for Peel Ports said the Port of Liverpool "plays a vital role in many critical supply chains from all over the world, handling products needed in the medical and healthcare sector, food industry and energy generation".
She added: "Customers who refuse to pay their bills put these other supply chains at risk.
"Any decision to detain a vessel is always taken as a last resort and only when there is a significant debt to repay."
Peel Ports said that the government had announced measures to support companies with "funding issues as a result of Covid-19".
It said: "Other ferry services from Liverpool to both Dublin and Belfast continue to operate, with multiple departures per day and spare capacity."