P&O Ferries has accused the Maritime and Coastguard Agency (MCA) of operating with "an unprecedented level of rigour" after it detained two of its ships.
European Causeway was held in Larne, Northern Ireland, on Friday, while Pride Of Kent was detained in Dover, Kent, on Monday.
Both ships failed inspections of emergency equipment, crew training and documentation.
The inspections are being carried out after P&O Ferries sacked nearly 800 seafarers on March 17 and replaced them with cheaper agency workers.
Trade unions and MPs have expressed fears that the controversial decision threatens safety.
A spokesman for P&O Ferries said: "It is clear that - following interventions by ministers and MPs - the MCA inspections have reached an unprecedented level of rigour, and we have been told that our ships will also now be required to pass further inspections by the flag state and classification society respectively.
"We welcome this additional scrutiny and would reiterate that the safety of our passengers and crew is our foremost priority.
"Any suggestion that it is being compromised in any way is categorically false and we look forward to all of our ships welcoming tourist passengers and freight customers again as soon as all mandatory safety tests have been passed."
An MCA spokeswoman said: "Our top priority is safety of shipping.
"We inspect without fear or favour every foreign flagged ship in exactly the same robust way under the regulations set out in Port State Control regime.
"Detentions under the Port State Control regime require that the flag state and operator put right any deficiencies before the MCA is invited to reinspect."
Transport Secretary Grant Shapps will announce a "package of measures" in the Commons on Wednesday which will include requiring seafarers working on ferries in the UK to be paid at least the minimum wage.
The minimum wage in the UK for people aged 23 and above is £8.91 per hour.
P&O Ferries chief executive Peter Hebblethwaite, whose basic annual salary is £325,000, told MPs on March 24 the average pay of the agency crew is £5.50 per hour.